# ignore compiled stuff
*.[oa]
+ cinfo.f
# ignore texteditors
*.swp
# ignore build dir
build/
+build2/
+ # latex files in documentation
+ doc/*/*.aux
+ doc/*/*.log
+
+
# ignored dirs form adasko
gradcheck/
mapcheck/
run/
sympcheck/
-compinfo
-DIL/
bin/unres/MD/unres_ifort_MPICH_GAB_czyt.exe
+bin/unres/MD-M/unres_Tc_procor_newparm_em64-D-symetr.exe
- DIL
++DIL/
+compinfo
evdw=0.0D0
evdw_t=0.0d0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
cd write (iout,*) 'i=',i,' iint=',iint,' istart=',istart(i,iint),
cd & 'iend=',iend(i,iint)
do j=istart(i,iint),iend(i,iint)
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
zj=c(3,nres+j)-zi
evdw=0.0D0
evdw_t=0.0d0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
C
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
zj=c(3,nres+j)-zi
c endif
ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
ind=ind+1
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
dscj_inv=vbld_inv(j+nres)
chi1=chi(itypi,itypj)
chi2=chi(itypj,itypi)
c if (icall.gt.0) lprn=.true.
ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
ind=ind+1
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
dscj_inv=vbld_inv(j+nres)
sig0ij=sigma(itypi,itypj)
chi1=chi(itypi,itypj)
c if (icall.gt.0) lprn=.true.
ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
ind=ind+1
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
dscj_inv=vbld_inv(j+nres)
sig0ij=sigma(itypi,itypj)
r0ij=r0(itypi,itypj)
gcorr_loc(i)=0.0d0
enddo
do i=iatel_s,iatel_e
- if (itype(i).eq.21 .or. itype(i+1).eq.21) cycle
+ if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
if (itel(i).eq.0) goto 1215
dxi=dc(1,i)
dyi=dc(2,i)
num_conti=0
c write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
do j=ielstart(i),ielend(i)
- if (itype(j).eq.21 .or. itype(j+1).eq.21) cycle
+ if (itype(j).eq.ntyp1 .or. itype(j+1).eq.ntyp1) cycle
if (itel(j).eq.0) goto 1216
ind=ind+1
iteli=itel(i)
& +0.5d0*(pizda(1,1)+pizda(2,2))
enddo
endif
- else if (j.eq.i+3 .and. itype(i+2).ne.21) then
+ else if (j.eq.i+3 .and. itype(i+2).ne.ntyp1) then
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
C
C Fourth-order contributions
c write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',iatscp_e,
c & ' scal14',scal14
do i=iatscp_s,iatscp_e
- if (itype(i).eq.21 .or. itype(i+1).eq.21) cycle
+ if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
iteli=itel(i)
c write (iout,*) "i",i," iteli",iteli," nscp_gr",nscp_gr(i),
c & " iscp",(iscpstart(i,j),iscpend(i,j),j=1,nscp_gr(i))
do iint=1,nscp_gr(i)
do j=iscpstart(i,iint),iscpend(i,iint)
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
C Uncomment following three lines for SC-p interactions
c xj=c(1,nres+j)-xi
c yj=c(2,nres+j)-yi
endif
C 24/11/03 AL: SS bridges handled separately because of introducing a specific
C distance and angle dependent SS bond potential.
- if (ii.gt.nres .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then
+ if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and.
+ & iabs(itype(jjj)).eq.1) then
call ssbond_ene(iii,jjj,eij)
ehpb=ehpb+2*eij
else
include 'COMMON.VAR'
include 'COMMON.IOUNITS'
double precision erij(3),dcosom1(3),dcosom2(3),gg(3)
- itypi=itype(i)
+ itypi=iabs(itype(i))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
dyi=dc_norm(2,nres+i)
dzi=dc_norm(3,nres+i)
dsci_inv=dsc_inv(itypi)
- itypj=itype(j)
+ itypj=iabs(itype(j))
dscj_inv=dsc_inv(itypj)
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
logical energy_dec /.false./
double precision u(3),ud(3)
estr=0.0d0
+ estr1=0.0d0
do i=nnt+1,nct
- if (itype(i-1).eq.21 .or. itype(i).eq.21) then
+ if (itype(i-1).eq.ntyp1 .or. itype(i).eq.ntyp1) then
estr1=estr1+gnmr1(vbld(i),-1.0d0,distchainmax)
do j=1,3
gradb(j,i-1)=gnmr1prim(vbld(i),-1.0d0,distchainmax)
endif
enddo
- estr=0.5d0*AKP*estr
+ estr=0.5d0*AKP*estr+estr1
c
c 09/18/07 AL: multimodal bond potential based on AM1 CA-SC PMF's included
c
do i=nnt,nct
- iti=itype(i)
- if (iti.ne.10 .and. iti.ne.21) then
+ iti=iabs(itype(i))
+ if (iti.ne.10 .and. iti.ne.ntyp1) then
nbi=nbondterm(iti)
if (nbi.eq.1) then
diff=vbld(i+nres)-vbldsc0(1,iti)
c write (*,'(a,i2)') 'EBEND ICG=',icg
c write (iout,*) ithet_start,ithet_end
do i=ithet_start,ithet_end
- if (itype(i-1).eq.21) cycle
+ if (itype(i-1).eq.ntyp1) cycle
C Zero the energy function and its derivative at 0 or pi.
call splinthet(theta(i),0.5d0*delta,ss,ssd)
it=itype(i-1)
- if (i.gt.3 .and. itype(i-2).ne.21) then
+ ichir1=isign(1,itype(i-2))
+ ichir2=isign(1,itype(i))
+ if (itype(i-2).eq.10) ichir1=isign(1,itype(i-1))
+ if (itype(i).eq.10) ichir2=isign(1,itype(i-1))
+ if (itype(i-1).eq.10) then
+ itype1=isign(10,itype(i-2))
+ ichir11=isign(1,itype(i-2))
+ ichir12=isign(1,itype(i-2))
+ itype2=isign(10,itype(i))
+ ichir21=isign(1,itype(i))
+ ichir22=isign(1,itype(i))
+ endif
+ if (i.gt.3 .and. itype(i-2).ne.ntyp1) then
#ifdef OSF
phii=phi(i)
icrc=0
y(1)=0.0D0
y(2)=0.0D0
endif
- if (i.lt.nres .and. itype(i).ne.21) then
+ if (i.lt.nres .and. itype(i).ne.ntyp1) then
#ifdef OSF
phii1=phi(i+1)
icrc=0
C In following comments this theta will be referred to as t_c.
thet_pred_mean=0.0d0
do k=1,2
- athetk=athet(k,it)
- bthetk=bthet(k,it)
+ athetk=athet(k,it,ichir1,ichir2)
+ bthetk=bthet(k,it,ichir1,ichir2)
+ if (it.eq.10) then
+ athetk=athet(k,itype1,ichir11,ichir12)
+ bthetk=bthet(k,itype2,ichir21,ichir22)
+ endif
thet_pred_mean=thet_pred_mean+athetk*y(k)+bthetk*z(k)
enddo
c write (iout,*) "thet_pred_mean",thet_pred_mean
thet_pred_mean=thet_pred_mean*ss+a0thet(it)
c write (iout,*) "thet_pred_mean",thet_pred_mean
C Derivatives of the "mean" values in gamma1 and gamma2.
- dthetg1=(-athet(1,it)*y(2)+athet(2,it)*y(1))*ss
- dthetg2=(-bthet(1,it)*z(2)+bthet(2,it)*z(1))*ss
+ dthetg1=(-athet(1,it,ichir1,ichir2)*y(2)
+ &+athet(2,it,ichir1,ichir2)*y(1))*ss
+ dthetg2=(-bthet(1,it,ichir1,ichir2)*z(2)
+ & +bthet(2,it,ichir1,ichir2)*z(1))*ss
+ if (it.eq.10) then
+ dthetg1=(-athet(1,itype1,ichir11,ichir12)*y(2)
+ &+athet(2,itype1,ichir11,ichir12)*y(1))*ss
+ dthetg2=(-bthet(1,itype2,ichir21,ichir22)*z(2)
+ & +bthet(2,itype2,ichir21,ichir22)*z(1))*ss
+ endif
if (theta(i).gt.pi-delta) then
call theteng(pi-delta,thet_pred_mean,theta0(it),f0,fprim0,
& E_tc0)
etheta=0.0D0
c write (iout,*) "ithetyp",(ithetyp(i),i=1,ntyp1)
do i=ithet_start,ithet_end
- if (itype(i-1).eq.21) cycle
+ if (itype(i-1).eq.ntyp1) cycle
+ if (iabs(itype(i+1)).eq.20) iblock=2
+ if (iabs(itype(i+1)).ne.20) iblock=1
dethetai=0.0d0
dephii=0.0d0
dephii1=0.0d0
theti2=0.5d0*theta(i)
- ityp2=ithetyp(itype(i-1))
+CC Ta zmina jest niewlasciwa
+ ityp2=ithetyp((itype(i-1)))
do k=1,nntheterm
coskt(k)=dcos(k*theti2)
sinkt(k)=dsin(k*theti2)
enddo
- if (i.gt.3 .and. itype(i-2).ne.21) then
+ if (i.gt.3 .and. itype(i-2).ne.ntyp1) then
#ifdef OSF
phii=phi(i)
if (phii.ne.phii) phii=150.0
#else
phii=phi(i)
#endif
- ityp1=ithetyp(itype(i-2))
+ ityp1=ithetyp((itype(i-2)))
do k=1,nsingle
cosph1(k)=dcos(k*phii)
sinph1(k)=dsin(k*phii)
sinph1(k)=0.0d0
enddo
endif
- if (i.lt.nres .and. itype(i).ne.21) then
+ if (i.lt.nres .and. itype(i).ne.ntyp1) then
#ifdef OSF
phii1=phi(i+1)
if (phii1.ne.phii1) phii1=150.0
#else
phii1=phi(i+1)
#endif
- ityp3=ithetyp(itype(i))
+ ityp3=ithetyp((itype(i)))
do k=1,nsingle
cosph2(k)=dcos(k*phii1)
sinph2(k)=dsin(k*phii1)
c write (iout,*) "i",i," ityp1",itype(i-2),ityp1,
c & " ityp2",itype(i-1),ityp2," ityp3",itype(i),ityp3
c call flush(iout)
- ethetai=aa0thet(ityp1,ityp2,ityp3)
+ ethetai=aa0thet(ityp1,ityp2,ityp3,iblock)
do k=1,ndouble
do l=1,k-1
ccl=cosph1(l)*cosph2(k-l)
enddo
endif
do k=1,ntheterm
- ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3)*sinkt(k)
- dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3)
+ ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3,iblock)*sinkt(k)
+ dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3,iblock)
& *coskt(k)
if (lprn)
- & write (iout,*) "k",k," aathet",aathet(k,ityp1,ityp2,ityp3),
+ & write (iout,*) "k",k," aathet",
+ & aathet(k,ityp1,ityp2,ityp3,iblock),
& " ethetai",ethetai
enddo
if (lprn) then
endif
do m=1,ntheterm2
do k=1,nsingle
- aux=bbthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)
- & +ccthet(k,m,ityp1,ityp2,ityp3)*sinph1(k)
- & +ddthet(k,m,ityp1,ityp2,ityp3)*cosph2(k)
- & +eethet(k,m,ityp1,ityp2,ityp3)*sinph2(k)
+ aux=bbthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k)
+ & +ccthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k)
+ & +ddthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k)
+ & +eethet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k)
ethetai=ethetai+sinkt(m)*aux
dethetai=dethetai+0.5d0*m*aux*coskt(m)
dephii=dephii+k*sinkt(m)*(
- & ccthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)-
- & bbthet(k,m,ityp1,ityp2,ityp3)*sinph1(k))
+ & ccthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k)-
+ & bbthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k))
dephii1=dephii1+k*sinkt(m)*(
- & eethet(k,m,ityp1,ityp2,ityp3)*cosph2(k)-
- & ddthet(k,m,ityp1,ityp2,ityp3)*sinph2(k))
+ & eethet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k)-
+ & ddthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k))
if (lprn)
& write (iout,*) "m",m," k",k," bbthet",
- & bbthet(k,m,ityp1,ityp2,ityp3)," ccthet",
- & ccthet(k,m,ityp1,ityp2,ityp3)," ddthet",
- & ddthet(k,m,ityp1,ityp2,ityp3)," eethet",
- & eethet(k,m,ityp1,ityp2,ityp3)," ethetai",ethetai
+ & bbthet(k,m,ityp1,ityp2,ityp3,iblock)," ccthet",
+ & ccthet(k,m,ityp1,ityp2,ityp3,iblock)," ddthet",
+ & ddthet(k,m,ityp1,ityp2,ityp3,iblock)," eethet",
+ & eethet(k,m,ityp1,ityp2,ityp3,iblock)," ethetai",ethetai
enddo
enddo
if (lprn)
do m=1,ntheterm3
do k=2,ndouble
do l=1,k-1
- aux=ffthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)
+ aux=ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)
ethetai=ethetai+sinkt(m)*aux
dethetai=dethetai+0.5d0*m*coskt(m)*aux
dephii=dephii+l*sinkt(m)*(
- & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)-
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+ & -ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)-
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l))
dephii1=dephii1+(k-l)*sinkt(m)*(
- & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)-
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+ & -ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)-
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l))
if (lprn) then
write (iout,*) "m",m," k",k," l",l," ffthet",
- & ffthet(l,k,m,ityp1,ityp2,ityp3),
- & ffthet(k,l,m,ityp1,ityp2,ityp3)," ggthet",
- & ggthet(l,k,m,ityp1,ityp2,ityp3),
- & ggthet(k,l,m,ityp1,ityp2,ityp3)," ethetai",ethetai
+ & ffthet(l,k,m,ityp1,ityp2,ityp3,iblock),
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)," ggthet",
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock),
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock),
+ & " ethetai",ethetai
write (iout,*) cosph1ph2(l,k)*sinkt(m),
& cosph1ph2(k,l)*sinkt(m),
& sinph1ph2(l,k)*sinkt(m),sinph1ph2(k,l)*sinkt(m)
c write (iout,'(a)') 'ESC'
do i=loc_start,loc_end
it=itype(i)
- if (it.eq.21) cycle
+ if (it.eq.ntyp1) cycle
if (it.eq.10) goto 1
- nlobit=nlob(it)
+ nlobit=nlob(iabs(it))
c print *,'i=',i,' it=',it,' nlobit=',nlobit
c write (iout,*) 'i=',i,' ssa=',ssa,' ssad=',ssad
theti=theta(i+1)-pipol
do iii=-1,1
do j=1,nlobit
- expfac=dexp(bsc(j,it)-0.5D0*contr(j,iii)+emin)
+ expfac=dexp(bsc(j,iabs(it))-0.5D0*contr(j,iii)+emin)
cd print *,'j=',j,' expfac=',expfac
escloc_i=escloc_i+expfac
do k=1,3
dersc12=0.0d0
do j=1,nlobit
- expfac=dexp(bsc(j,it)-0.5D0*contr(j)+emin)
+ expfac=dexp(bsc(j,iabs(it))-0.5D0*contr(j)+emin)
escloc_i=escloc_i+expfac
do k=1,2
dersc(k)=dersc(k)+Ax(k,j)*expfac
delta=0.02d0*pi
escloc=0.0D0
do i=loc_start,loc_end
- if (itype(i).eq.21) cycle
+ if (itype(i).eq.ntyp1) cycle
costtab(i+1) =dcos(theta(i+1))
sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
cosfac=dsqrt(cosfac2)
sinfac2=0.5d0/(1.0d0-costtab(i+1))
sinfac=dsqrt(sinfac2)
- it=itype(i)
+ it=iabs(itype(i))
if (it.eq.10) goto 1
c
C Compute the axes of tghe local cartesian coordinates system; store in
y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
enddo
do j = 1,3
- z_prime(j) = -uz(j,i-1)
+ z_prime(j) = -uz(j,i-1)*dsign(1.0d0,dfloat(itype(i)))
enddo
c write (2,*) "i",i
c write (2,*) "x_prime",(x_prime(j),j=1,3)
C Compute the energy of the ith side cbain
C
c write (2,*) "xx",xx," yy",yy," zz",zz
- it=itype(i)
+ it=iabs(itype(i))
do j = 1,65
x(j) = sc_parmin(j,it)
enddo
dZZ_Ci1(k)=0.0d0
dZZ_Ci(k)=0.0d0
do j=1,3
- dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)*dC_norm(j,i+nres)
- dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)*dC_norm(j,i+nres)
+ dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)
+ & *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres)
+ dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)
+ & *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres)
enddo
dXX_XYZ(k)=vbld_inv(i+nres)*(x_prime(k)-xx*dC_norm(k,i+nres))
c lprn=.true.
etors=0.0D0
do i=iphi_start,iphi_end
- if (itype(i-2).eq.21 .or. itype(i-1).eq.21
- & .or. itype(i).eq.21) cycle
+ if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1
+ & .or. itype(i).eq.ntyp1) cycle
itori=itortyp(itype(i-2))
itori1=itortyp(itype(i-1))
phii=phi(i)
c lprn=.true.
etors=0.0D0
do i=iphi_start,iphi_end
- if (itype(i-2).eq.21 .or. itype(i-1).eq.21
- & .or. itype(i).eq.21) cycle
+ if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1
+ & .or. itype(i).eq.ntyp1) cycle
if (itel(i-2).eq.0 .or. itel(i-1).eq.0) goto 1215
+ if (iabs(itype(i)).eq.20) then
+ iblock=2
+ else
+ iblock=1
+ endif
itori=itortyp(itype(i-2))
itori1=itortyp(itype(i-1))
phii=phi(i)
gloci=0.0D0
C Regular cosine and sine terms
- do j=1,nterm(itori,itori1)
- v1ij=v1(j,itori,itori1)
- v2ij=v2(j,itori,itori1)
+ do j=1,nterm(itori,itori1,iblock)
+ v1ij=v1(j,itori,itori1,iblock)
+ v2ij=v2(j,itori,itori1,iblock)
cosphi=dcos(j*phii)
sinphi=dsin(j*phii)
etors=etors+v1ij*cosphi+v2ij*sinphi
C
cosphi=dcos(0.5d0*phii)
sinphi=dsin(0.5d0*phii)
- do j=1,nlor(itori,itori1)
+ do j=1,nlor(itori,itori1,iblock)
vl1ij=vlor1(j,itori,itori1)
vl2ij=vlor2(j,itori,itori1)
vl3ij=vlor3(j,itori,itori1)
gloci=gloci+vl1ij*(vl3ij*cosphi-vl2ij*sinphi)*pom
enddo
C Subtract the constant term
- etors=etors-v0(itori,itori1)
+ etors=etors-v0(itori,itori1,iblock)
if (lprn)
& write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)')
& restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
- & (v1(j,itori,itori1),j=1,6),(v2(j,itori,itori1),j=1,6)
+ & (v1(j,itori,itori1,1),j=1,6),(v2(j,itori,itori1,1),j=1,6)
gloc(i-3,icg)=gloc(i-3,icg)+wtor*fact*gloci
c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg)
1215 continue
c lprn=.true.
etors_d=0.0D0
do i=iphi_start,iphi_end-1
- if (itype(i-2).eq.21 .or. itype(i-1).eq.21
- & .or. itype(i).eq.21 .or. itype(i+1).eq.21) cycle
+ if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1
+ & .or. itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
if (itel(i-2).eq.0 .or. itel(i-1).eq.0 .or. itel(i).eq.0)
& goto 1215
itori=itortyp(itype(i-2))
phii1=phi(i+1)
gloci1=0.0D0
gloci2=0.0D0
+ iblock=1
+ if (iabs(itype(i+1)).eq.20) iblock=2
C Regular cosine and sine terms
- do j=1,ntermd_1(itori,itori1,itori2)
- v1cij=v1c(1,j,itori,itori1,itori2)
- v1sij=v1s(1,j,itori,itori1,itori2)
- v2cij=v1c(2,j,itori,itori1,itori2)
- v2sij=v1s(2,j,itori,itori1,itori2)
+ do j=1,ntermd_1(itori,itori1,itori2,iblock)
+ v1cij=v1c(1,j,itori,itori1,itori2,iblock)
+ v1sij=v1s(1,j,itori,itori1,itori2,iblock)
+ v2cij=v1c(2,j,itori,itori1,itori2,iblock)
+ v2sij=v1s(2,j,itori,itori1,itori2,iblock)
cosphi1=dcos(j*phii)
sinphi1=dsin(j*phii)
cosphi2=dcos(j*phii1)
gloci1=gloci1+j*(v1sij*cosphi1-v1cij*sinphi1)
gloci2=gloci2+j*(v2sij*cosphi2-v2cij*sinphi2)
enddo
- do k=2,ntermd_2(itori,itori1,itori2)
+ do k=2,ntermd_2(itori,itori1,itori2,iblock)
do l=1,k-1
- v1cdij = v2c(k,l,itori,itori1,itori2)
- v2cdij = v2c(l,k,itori,itori1,itori2)
- v1sdij = v2s(k,l,itori,itori1,itori2)
- v2sdij = v2s(l,k,itori,itori1,itori2)
+ v1cdij = v2c(k,l,itori,itori1,itori2,iblock)
+ v2cdij = v2c(l,k,itori,itori1,itori2,iblock)
+ v1sdij = v2s(k,l,itori,itori1,itori2,iblock)
+ v2sdij = v2s(l,k,itori,itori1,itori2,iblock)
cosphi1p2=dcos(l*phii+(k-l)*phii1)
cosphi1m2=dcos(l*phii-(k-l)*phii1)
sinphi1p2=dsin(l*phii+(k-l)*phii1)
c lprn=.true.
c write (iout,*) "EBACK_SC_COR",iphi_start,iphi_end,nterm_sccor
esccor=0.0D0
- do i=iphi_start,iphi_end
- if (itype(i-2).eq.21 .or. itype(i-1).eq.21) cycle
+ do i=itau_start,itau_end
+ if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1) cycle
esccor_ii=0.0D0
- itori=itype(i-2)
- itori1=itype(i-1)
+ isccori=isccortyp(itype(i-2))
+ isccori1=isccortyp(itype(i-1))
phii=phi(i)
+ do intertyp=1,3 !intertyp
+cc Added 09 May 2012 (Adasko)
+cc Intertyp means interaction type of backbone mainchain correlation:
+c 1 = SC...Ca...Ca...Ca
+c 2 = Ca...Ca...Ca...SC
+c 3 = SC...Ca...Ca...SCi
gloci=0.0D0
- do j=1,nterm_sccor
- v1ij=v1sccor(j,itori,itori1)
- v2ij=v2sccor(j,itori,itori1)
- cosphi=dcos(j*phii)
- sinphi=dsin(j*phii)
- esccor=esccor+v1ij*cosphi+v2ij*sinphi
- gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
- enddo
+ if (((intertyp.eq.3).and.((itype(i-2).eq.10).or.
+ & (itype(i-1).eq.10).or.(itype(i-2).eq.ntyp1).or.
+ & (itype(i-1).eq.ntyp1)))
+ & .or. ((intertyp.eq.1).and.((itype(i-2).eq.10)
+ & .or.(itype(i-2).eq.ntyp1).or.(itype(i-1).eq.ntyp1)
+ & .or.(itype(i).eq.ntyp1)))
+ & .or.((intertyp.eq.2).and.((itype(i-1).eq.10).or.
+ & (itype(i-1).eq.ntyp1).or.(itype(i-2).eq.ntyp1).or.
+ & (itype(i-3).eq.ntyp1)))) cycle
+ if ((intertyp.eq.2).and.(i.eq.4).and.(itype(1).eq.ntyp1)) cycle
+ if ((intertyp.eq.1).and.(i.eq.nres).and.(itype(nres).eq.ntyp1))
+ & cycle
+ do j=1,nterm_sccor(isccori,isccori1)
+ v1ij=v1sccor(j,intertyp,isccori,isccori1)
+ v2ij=v2sccor(j,intertyp,isccori,isccori1)
+ cosphi=dcos(j*tauangle(intertyp,i))
+ sinphi=dsin(j*tauangle(intertyp,i))
+ esccor=esccor+v1ij*cosphi+v2ij*sinphi
+c gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
+ enddo
+c write (iout,*) "EBACK_SC_COR",i,esccor,intertyp
+c gloc_sc(intertyp,i-3)=gloc_sc(intertyp,i-3)+wsccor*gloci
if (lprn)
& write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)')
& restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
- & (v1sccor(j,itori,itori1),j=1,6),(v2sccor(j,itori,itori1),j=1,6)
+ & (v1sccor(j,1,itori,itori1),j=1,6),
+ & (v2sccor(j,1,itori,itori1),j=1,6)
gsccor_loc(i-3)=gloci
+ enddo !intertyp
enddo
return
end
include 'COMMON.GEO'
logical swap
double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2),
- & auxvec1(2),auxvec2(1),auxmat1(2,2)
+ & auxvec1(2),auxvec2(2),auxmat1(2,2)
logical lprn
common /kutas/ lprn
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
#ifdef SPLITELE
etot=wsc*evdw+wscp*evdw2+welec*fact(1)*ees+wvdwpp*evdw1
& +wang*ebe+wtor*fact(1)*etors+wscloc*escloc
- & +wstrain*ehpb+nss*ebr+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5
+ & +wstrain*ehpb+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5
& +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4
& +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6
& +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d
#else
etot=wsc*evdw+wscp*evdw2+welec*fact(1)*(ees+evdw1)
& +wang*ebe+wtor*fact(1)*etors+wscloc*escloc
- & +wstrain*ehpb+nss*ebr+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5
+ & +wstrain*ehpb+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5
& +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4
& +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6
& +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d
energia(18)=estr
energia(19)=esccor
energia(20)=edihcnstr
+ cc if (dyn_ss) call dyn_set_nss
c detecting NaNQ
i=0
#ifdef WINPGI
& +wturn4*fact(3)*gel_loc_turn4(i)
& +wturn3*fact(2)*gel_loc_turn3(i)
& +wturn6*fact(5)*gel_loc_turn6(i)
- & +wel_loc*fact(2)*gel_loc_loc(i)+
+ & +wel_loc*fact(2)*gel_loc_loc(i)
& +wsccor*fact(1)*gsccor_loc(i)
enddo
endif
cd print *,'Entering ELJ nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
cd write (iout,*) 'i=',i,' iint=',iint,' istart=',istart(i,iint),
cd & 'iend=',iend(i,iint)
do j=istart(i,iint),iend(i,iint)
- itypj=itype(j)
+ itypj=iabs(itype(j))
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
zj=c(3,nres+j)-zi
c print *,'Entering ELJK nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
C
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
- itypj=itype(j)
+ itypj=iabs(itype(j))
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
zj=c(3,nres+j)-zi
c endif
ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
ind=ind+1
- itypj=itype(j)
+ itypj=iabs(itype(j))
dscj_inv=vbld_inv(j+nres)
chi1=chi(itypi,itypj)
chi2=chi(itypj,itypi)
include 'COMMON.INTERACT'
include 'COMMON.IOUNITS'
include 'COMMON.CALC'
+ include 'COMMON.SBRIDGE'
logical lprn
common /srutu/icall
integer icant
c if (icall.gt.0) lprn=.true.
ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
C
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
+ IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN
+ call dyn_ssbond_ene(i,j,evdwij)
+ evdw=evdw+evdwij
+ c if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)')
+ c & 'evdw',i,j,evdwij,' ss'
+ ELSE
ind=ind+1
- itypj=itype(j)
+ itypj=iabs(itype(j))
dscj_inv=vbld_inv(j+nres)
sig0ij=sigma(itypi,itypj)
chi1=chi(itypi,itypj)
C Calculate angular part of the gradient.
call sc_grad
endif
+ ENDIF ! SSBOND
enddo ! j
enddo ! iint
enddo ! i
include 'COMMON.INTERACT'
include 'COMMON.IOUNITS'
include 'COMMON.CALC'
+ include 'COMMON.SBRIDGE'
common /srutu/ icall
logical lprn
integer icant
c if (icall.gt.0) lprn=.true.
ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
C
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
+ C in case of diagnostics write (iout,*) "TU SZUKAJ",i,j,dyn_ss_mask(i),dyn_ss_mask(j)
+ IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN
+ call dyn_ssbond_ene(i,j,evdwij)
+ evdw=evdw+evdwij
+ c if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)')
+ c & 'evdw',i,j,evdwij,' ss'
+ ELSE
ind=ind+1
- itypj=itype(j)
+ itypj=iabs(itype(j))
dscj_inv=vbld_inv(j+nres)
sig0ij=sigma(itypi,itypj)
r0ij=r0(itypi,itypj)
C Calculate angular part of the gradient.
call sc_grad
endif
+ ENDIF ! dyn_ss
enddo ! j
enddo ! iint
enddo ! i
do iint=1,nscp_gr(i)
do j=iscpstart(i,iint),iscpend(i,iint)
- itypj=itype(j)
+ itypj=iabs(itype(j))
C Uncomment following three lines for SC-p interactions
c xj=c(1,nres+j)-xi
c yj=c(2,nres+j)-yi
c & dhpb(i),dhpb1(i),forcon(i)
C 24/11/03 AL: SS bridges handled separately because of introducing a specific
C distance and angle dependent SS bond potential.
+ if (.not.dyn_ss .and. i.le.nss) then
+ C 15/02/13 CC dynamic SSbond - additional check
- if (ii.gt.nres .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then
+ if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and.
+ & iabs( itype(jjj)).eq.1) then
call ssbond_ene(iii,jjj,eij)
ehpb=ehpb+2*eij
cd write (iout,*) "eij",eij
+ endif
else if (ii.gt.nres .and. jj.gt.nres) then
c Restraints from contact prediction
dd=dist(ii,jj)
include 'COMMON.VAR'
include 'COMMON.IOUNITS'
double precision erij(3),dcosom1(3),dcosom2(3),gg(3)
- itypi=itype(i)
+ itypi=iabs(itype(i))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
dyi=dc_norm(2,nres+i)
dzi=dc_norm(3,nres+i)
dsci_inv=dsc_inv(itypi)
- itypj=itype(j)
+ itypj=iabs(itype(j))
dscj_inv=dsc_inv(itypj)
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
deltat12=om2-om1+2.0d0
cosphi=om12-om1*om2
eij=akcm*deltad*deltad+akth*(deltat1*deltat1+deltat2*deltat2)
- & +akct*deltad*deltat12
+ & +akct*deltad*deltat12+ebr
& +v1ss*cosphi+v2ss*cosphi*cosphi+v3ss*cosphi*cosphi*cosphi
c write(iout,*) i,j,"rij",rij,"d0cm",d0cm," akcm",akcm," akth",akth,
c & " akct",akct," deltad",deltad," deltat",deltat1,deltat2,
c 09/18/07 AL: multimodal bond potential based on AM1 CA-SC PMF's included
c
do i=nnt,nct
- iti=itype(i)
+ iti=iabs(itype(i))
if (iti.ne.10) then
nbi=nbondterm(iti)
if (nbi.eq.1) then
C Zero the energy function and its derivative at 0 or pi.
call splinthet(theta(i),0.5d0*delta,ss,ssd)
it=itype(i-1)
+ ichir1=isign(1,itype(i-2))
+ ichir2=isign(1,itype(i))
+ if (itype(i-2).eq.10) ichir1=isign(1,itype(i-1))
+ if (itype(i).eq.10) ichir2=isign(1,itype(i-1))
+ if (itype(i-1).eq.10) then
+ itype1=isign(10,itype(i-2))
+ ichir11=isign(1,itype(i-2))
+ ichir12=isign(1,itype(i-2))
+ itype2=isign(10,itype(i))
+ ichir21=isign(1,itype(i))
+ ichir22=isign(1,itype(i))
+ endif
c if (i.gt.ithet_start .and.
c & (itel(i-1).eq.0 .or. itel(i-2).eq.0)) goto 1215
c if (i.gt.3 .and. (i.le.4 .or. itel(i-3).ne.0)) then
C In following comments this theta will be referred to as t_c.
thet_pred_mean=0.0d0
do k=1,2
- athetk=athet(k,it)
- bthetk=bthet(k,it)
+ athetk=athet(k,it,ichir1,ichir2)
+ bthetk=bthet(k,it,ichir1,ichir2)
+ if (it.eq.10) then
+ athetk=athet(k,itype1,ichir11,ichir12)
+ bthetk=bthet(k,itype2,ichir21,ichir22)
+ endif
thet_pred_mean=thet_pred_mean+athetk*y(k)+bthetk*z(k)
enddo
c write (iout,*) "thet_pred_mean",thet_pred_mean
thet_pred_mean=thet_pred_mean*ss+a0thet(it)
c write (iout,*) "thet_pred_mean",thet_pred_mean
C Derivatives of the "mean" values in gamma1 and gamma2.
- dthetg1=(-athet(1,it)*y(2)+athet(2,it)*y(1))*ss
- dthetg2=(-bthet(1,it)*z(2)+bthet(2,it)*z(1))*ss
+ dthetg1=(-athet(1,it,ichir1,ichir2)*y(2)
+ &+athet(2,it,ichir1,ichir2)*y(1))*ss
+ dthetg2=(-bthet(1,it,ichir1,ichir2)*z(2)
+ & +bthet(2,it,ichir1,ichir2)*z(1))*ss
+ if (it.eq.10) then
+ dthetg1=(-athet(1,itype1,ichir11,ichir12)*y(2)
+ &+athet(2,itype1,ichir11,ichir12)*y(1))*ss
+ dthetg2=(-bthet(1,itype2,ichir21,ichir22)*z(2)
+ & +bthet(2,itype2,ichir21,ichir22)*z(1))*ss
+ endif
if (theta(i).gt.pi-delta) then
call theteng(pi-delta,thet_pred_mean,theta0(it),f0,fprim0,
& E_tc0)
etheta=0.0D0
c write (iout,*) "ithetyp",(ithetyp(i),i=1,ntyp1)
do i=ithet_start,ithet_end
+ if (itype(i-1).eq.ntyp1) cycle
+ if (iabs(itype(i+1)).eq.20) iblock=2
+ if (iabs(itype(i+1)).ne.20) iblock=1
dethetai=0.0d0
dephii=0.0d0
dephii1=0.0d0
theti2=0.5d0*theta(i)
- ityp2=ithetyp(itype(i-1))
+ ityp2=ithetyp((itype(i-1)))
do k=1,nntheterm
coskt(k)=dcos(k*theti2)
sinkt(k)=dsin(k*theti2)
#else
phii=phi(i)
#endif
- ityp1=ithetyp(itype(i-2))
+ ityp1=ithetyp((itype(i-2)))
do k=1,nsingle
cosph1(k)=dcos(k*phii)
sinph1(k)=dsin(k*phii)
#else
phii1=phi(i+1)
#endif
- ityp3=ithetyp(itype(i))
+ ityp3=ithetyp((itype(i)))
do k=1,nsingle
cosph2(k)=dcos(k*phii1)
sinph2(k)=dsin(k*phii1)
c write (iout,*) "i",i," ityp1",itype(i-2),ityp1,
c & " ityp2",itype(i-1),ityp2," ityp3",itype(i),ityp3
c call flush(iout)
- ethetai=aa0thet(ityp1,ityp2,ityp3)
+ ethetai=aa0thet(ityp1,ityp2,ityp3,iblock)
do k=1,ndouble
do l=1,k-1
ccl=cosph1(l)*cosph2(k-l)
enddo
endif
do k=1,ntheterm
- ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3)*sinkt(k)
- dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3)
+ ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3,iblock)*sinkt(k)
+ dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3,iblock)
& *coskt(k)
if (lprn)
- & write (iout,*) "k",k," aathet",aathet(k,ityp1,ityp2,ityp3),
+ & write (iout,*) "k",k," aathet"
+ & ,aathet(k,ityp1,ityp2,ityp3,iblock),
& " ethetai",ethetai
enddo
if (lprn) then
endif
do m=1,ntheterm2
do k=1,nsingle
- aux=bbthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)
- & +ccthet(k,m,ityp1,ityp2,ityp3)*sinph1(k)
- & +ddthet(k,m,ityp1,ityp2,ityp3)*cosph2(k)
- & +eethet(k,m,ityp1,ityp2,ityp3)*sinph2(k)
+ aux=bbthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k)
+ & +ccthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k)
+ & +ddthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k)
+ & +eethet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k)
ethetai=ethetai+sinkt(m)*aux
dethetai=dethetai+0.5d0*m*aux*coskt(m)
dephii=dephii+k*sinkt(m)*(
- & ccthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)-
- & bbthet(k,m,ityp1,ityp2,ityp3)*sinph1(k))
+ & ccthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k)-
+ & bbthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k))
dephii1=dephii1+k*sinkt(m)*(
- & eethet(k,m,ityp1,ityp2,ityp3)*cosph2(k)-
- & ddthet(k,m,ityp1,ityp2,ityp3)*sinph2(k))
+ & eethet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k)-
+ & ddthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k))
if (lprn)
& write (iout,*) "m",m," k",k," bbthet",
- & bbthet(k,m,ityp1,ityp2,ityp3)," ccthet",
- & ccthet(k,m,ityp1,ityp2,ityp3)," ddthet",
- & ddthet(k,m,ityp1,ityp2,ityp3)," eethet",
- & eethet(k,m,ityp1,ityp2,ityp3)," ethetai",ethetai
+ & bbthet(k,m,ityp1,ityp2,ityp3,iblock)," ccthet",
+ & ccthet(k,m,ityp1,ityp2,ityp3,iblock)," ddthet",
+ & ddthet(k,m,ityp1,ityp2,ityp3,iblock)," eethet",
+ & eethet(k,m,ityp1,ityp2,ityp3,iblock)," ethetai",ethetai
enddo
enddo
if (lprn)
do m=1,ntheterm3
do k=2,ndouble
do l=1,k-1
- aux=ffthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)
+ aux=ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)
ethetai=ethetai+sinkt(m)*aux
dethetai=dethetai+0.5d0*m*coskt(m)*aux
dephii=dephii+l*sinkt(m)*(
- & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)-
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+ & -ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)-
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l))
dephii1=dephii1+(k-l)*sinkt(m)*(
- & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)-
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+ & -ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)-
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l))
if (lprn) then
write (iout,*) "m",m," k",k," l",l," ffthet",
- & ffthet(l,k,m,ityp1,ityp2,ityp3),
- & ffthet(k,l,m,ityp1,ityp2,ityp3)," ggthet",
- & ggthet(l,k,m,ityp1,ityp2,ityp3),
- & ggthet(k,l,m,ityp1,ityp2,ityp3)," ethetai",ethetai
+ & ffthet(l,k,m,ityp1,ityp2,ityp3,iblock),
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)," ggthet",
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock),
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)," ethetai",
+ & ethetai
write (iout,*) cosph1ph2(l,k)*sinkt(m),
& cosph1ph2(k,l)*sinkt(m),
& sinph1ph2(l,k)*sinkt(m),sinph1ph2(k,l)*sinkt(m)
do i=loc_start,loc_end
it=itype(i)
if (it.eq.10) goto 1
- nlobit=nlob(it)
+ nlobit=nlob(iabs(it))
c print *,'i=',i,' it=',it,' nlobit=',nlobit
c write (iout,*) 'i=',i,' ssa=',ssa,' ssad=',ssad
theti=theta(i+1)-pipol
do iii=-1,1
do j=1,nlobit
- expfac=dexp(bsc(j,it)-0.5D0*contr(j,iii)+emin)
+ expfac=dexp(bsc(j,iabs(it))-0.5D0*contr(j,iii)+emin)
cd print *,'j=',j,' expfac=',expfac
escloc_i=escloc_i+expfac
do k=1,3
dersc12=0.0d0
do j=1,nlobit
- expfac=dexp(bsc(j,it)-0.5D0*contr(j)+emin)
+ expfac=dexp(bsc(j,iabs(it))-0.5D0*contr(j)+emin)
escloc_i=escloc_i+expfac
do k=1,2
dersc(k)=dersc(k)+Ax(k,j)*expfac
cosfac=dsqrt(cosfac2)
sinfac2=0.5d0/(1.0d0-costtab(i+1))
sinfac=dsqrt(sinfac2)
- it=itype(i)
+ it=iabs(itype(i))
if (it.eq.10) goto 1
c
C Compute the axes of tghe local cartesian coordinates system; store in
y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
enddo
do j = 1,3
- z_prime(j) = -uz(j,i-1)
+ z_prime(j) = -uz(j,i-1)*dsign(1.0d0,dfloat(itype(i)))
enddo
c write (2,*) "i",i
c write (2,*) "x_prime",(x_prime(j),j=1,3)
xx = xx + x_prime(j)*dc_norm(j,i+nres)
yy = yy + y_prime(j)*dc_norm(j,i+nres)
zz = zz + z_prime(j)*dc_norm(j,i+nres)
+ zz = zz + z_prime(j)*dc_norm(j,i+nres)
enddo
xxtab(i)=xx
yytab(i)=yy
zztab(i)=zz
+
C
C Compute the energy of the ith side cbain
C
c write (2,*) "xx",xx," yy",yy," zz",zz
- it=itype(i)
+ it=iabs(itype(i))
do j = 1,65
x(j) = sc_parmin(j,it)
enddo
dZZ_Ci1(k)=0.0d0
dZZ_Ci(k)=0.0d0
do j=1,3
- dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)*dC_norm(j,i+nres)
- dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)*dC_norm(j,i+nres)
+ dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)
+ & *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres)
+ dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)
+ & *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres)
enddo
dXX_XYZ(k)=vbld_inv(i+nres)*(x_prime(k)-xx*dC_norm(k,i+nres))
etors=0.0D0
do i=iphi_start,iphi_end
if (itel(i-2).eq.0 .or. itel(i-1).eq.0) goto 1215
+ if (iabs(itype(i)).eq.20) then
+ iblock=2
+ else
+ iblock=1
+ endif
itori=itortyp(itype(i-2))
itori1=itortyp(itype(i-1))
phii=phi(i)
gloci=0.0D0
C Regular cosine and sine terms
- do j=1,nterm(itori,itori1)
- v1ij=v1(j,itori,itori1)
- v2ij=v2(j,itori,itori1)
+ do j=1,nterm(itori,itori1,iblock)
+ v1ij=v1(j,itori,itori1,iblock)
+ v2ij=v2(j,itori,itori1,iblock)
cosphi=dcos(j*phii)
sinphi=dsin(j*phii)
etors=etors+v1ij*cosphi+v2ij*sinphi
C
cosphi=dcos(0.5d0*phii)
sinphi=dsin(0.5d0*phii)
- do j=1,nlor(itori,itori1)
+ do j=1,nlor(itori,itori1,iblock)
vl1ij=vlor1(j,itori,itori1)
vl2ij=vlor2(j,itori,itori1)
vl3ij=vlor3(j,itori,itori1)
gloci=gloci+vl1ij*(vl3ij*cosphi-vl2ij*sinphi)*pom
enddo
C Subtract the constant term
- etors=etors-v0(itori,itori1)
+ etors=etors-v0(itori,itori1,iblock)
if (lprn)
& write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)')
& restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
- & (v1(j,itori,itori1),j=1,6),(v2(j,itori,itori1),j=1,6)
+ & (v1(j,itori,itori1,1),j=1,6),(v2(j,itori,itori1,1),j=1,6)
gloc(i-3,icg)=gloc(i-3,icg)+wtor*fact*gloci
c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg)
1215 continue
phii1=phi(i+1)
gloci1=0.0D0
gloci2=0.0D0
+ iblock=1
+ if (iabs(itype(i+1)).eq.20) iblock=2
C Regular cosine and sine terms
- do j=1,ntermd_1(itori,itori1,itori2)
- v1cij=v1c(1,j,itori,itori1,itori2)
- v1sij=v1s(1,j,itori,itori1,itori2)
- v2cij=v1c(2,j,itori,itori1,itori2)
- v2sij=v1s(2,j,itori,itori1,itori2)
+ do j=1,ntermd_1(itori,itori1,itori2,iblock)
+ v1cij=v1c(1,j,itori,itori1,itori2,iblock)
+ v1sij=v1s(1,j,itori,itori1,itori2,iblock)
+ v2cij=v1c(2,j,itori,itori1,itori2,iblock)
+ v2sij=v1s(2,j,itori,itori1,itori2,iblock)
cosphi1=dcos(j*phii)
sinphi1=dsin(j*phii)
cosphi2=dcos(j*phii1)
gloci1=gloci1+j*(v1sij*cosphi1-v1cij*sinphi1)
gloci2=gloci2+j*(v2sij*cosphi2-v2cij*sinphi2)
enddo
- do k=2,ntermd_2(itori,itori1,itori2)
+ do k=2,ntermd_2(itori,itori1,itori2,iblock)
do l=1,k-1
- v1cdij = v2c(k,l,itori,itori1,itori2)
- v2cdij = v2c(l,k,itori,itori1,itori2)
- v1sdij = v2s(k,l,itori,itori1,itori2)
- v2sdij = v2s(l,k,itori,itori1,itori2)
+ v1cdij = v2c(k,l,itori,itori1,itori2,iblock)
+ v2cdij = v2c(l,k,itori,itori1,itori2,iblock)
+ v1sdij = v2s(k,l,itori,itori1,itori2,iblock)
+ v2sdij = v2s(l,k,itori,itori1,itori2,iblock)
cosphi1p2=dcos(l*phii+(k-l)*phii1)
cosphi1m2=dcos(l*phii-(k-l)*phii1)
sinphi1p2=dsin(l*phii+(k-l)*phii1)
c 3 = SC...Ca...Ca...SCi
gloci=0.0D0
if (((intertyp.eq.3).and.((itype(i-2).eq.10).or.
- & (itype(i-1).eq.10).or.(itype(i-2).eq.21).or.
- & (itype(i-1).eq.21)))
+ & (itype(i-1).eq.10).or.(itype(i-2).eq.ntyp1).or.
+ & (itype(i-1).eq.ntyp1)))
& .or. ((intertyp.eq.1).and.((itype(i-2).eq.10)
- & .or.(itype(i-2).eq.21)))
+ & .or.(itype(i-2).eq.ntyp1)))
& .or.((intertyp.eq.2).and.((itype(i-1).eq.10).or.
- & (itype(i-1).eq.21)))) cycle
- if ((intertyp.eq.2).and.(i.eq.4).and.(itype(1).eq.21)) cycle
- if ((intertyp.eq.1).and.(i.eq.nres).and.(itype(nres).eq.21))
+ & (itype(i-1).eq.ntyp1)))) cycle
+ if ((intertyp.eq.2).and.(i.eq.4).and.(itype(1).eq.ntyp1)) cycle
+ if ((intertyp.eq.1).and.(i.eq.nres).and.(itype(nres).eq.ntyp1))
& cycle
do j=1,nterm_sccor(isccori,isccori1)
v1ij=v1sccor(j,intertyp,isccori,isccori1)
C Set lprn=.true. for debugging
lprn=.false.
eturn6=0.0d0
+ ecorr6=0.0d0
#ifdef MPL
n_corr=0
n_corr1=0
cd write(2,*)'ijkl',i,j,i+1,j1
if (wcorr6.gt.0.0d0 .and. (j.ne.i+4 .or. j1.ne.i+3
& .or. wturn6.eq.0.0d0))then
- cd write (iout,*) '******ecorr6: i,j,i+1,j1',i,j,i+1,j1
- ecorr6=ecorr6+eello6(i,j,i+1,j1,jj,kk)
- cd write (iout,*) 'ecorr',ecorr,' ecorr5=',ecorr5,
- cd & 'ecorr6=',ecorr6
+ c write (iout,*) '******ecorr6: i,j,i+1,j1',i,j,i+1,j1
+ c ecorr6=ecorr6+eello6(i,j,i+1,j1,jj,kk)
+ c write (iout,*) 'ecorr',ecorr,' ecorr5=',ecorr5,
+ c & 'ecorr6=',ecorr6, wcorr6
cd write (iout,'(4e15.5)') sred_geom,
cd & dabs(eello4(i,j,i+1,j1,jj,kk)),
cd & dabs(eello5(i,j,i+1,j1,jj,kk)),
include 'COMMON.GEO'
logical swap
double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2),
- & auxvec1(2),auxvec2(1),auxmat1(2,2)
+ & auxvec1(2),auxvec2(2),auxmat1(2,2)
logical lprn
common /kutas/ lprn
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
sigii(i)=0.0D0
rr0(i)=0.0D0
a0thet(i)=0.0D0
- do j=1,2
- athet(j,i)=0.0D0
- bthet(j,i)=0.0D0
+ do j=1,2
+ do ichir1=-1,1
+ do ichir2=-1,1
+ athet(j,i,ichir1,ichir2)=0.0D0
+ bthet(j,i,ichir1,ichir2)=0.0D0
+ enddo
+ enddo
enddo
do j=0,3
polthet(j,i)=0.0D0
enddo
nlob(ntyp1)=0
dsc(ntyp1)=0.0D0
- do i=1,maxtor
+ do i=-maxtor,maxtor
itortyp(i)=0
- do j=1,maxtor
- do k=1,maxterm
- v1(k,j,i)=0.0D0
- v2(k,j,i)=0.0D0
- enddo
+ do iblock=1,2
+ do j=-maxtor,maxtor
+ do k=1,maxterm
+ v1(k,j,i,iblock)=0.0D0
+ v2(k,j,i,iblock)=0.0D0
+ enddo
+ enddo
enddo
enddo
+ do iblock=1,2
+ do i=-maxtor,maxtor
+ do j=-maxtor,maxtor
+ do k=-maxtor,maxtor
+ do l=1,maxtermd_1
+ v1c(1,l,i,j,k,iblock)=0.0D0
+ v1s(1,l,i,j,k,iblock)=0.0D0
+ v1c(2,l,i,j,k,iblock)=0.0D0
+ v1s(2,l,i,j,k,iblock)=0.0D0
+ enddo !l
+ do l=1,maxtermd_2
+ do m=1,maxtermd_2
+ v2c(m,l,i,j,k,iblock)=0.0D0
+ v2s(m,l,i,j,k,iblock)=0.0D0
+ enddo !m
+ enddo !l
+ enddo !k
+ enddo !j
+ enddo !i
+ enddo !iblock
do i=1,maxres
itype(i)=0
itel(i)=0
ihpb(i)=0
jhpb(i)=0
enddo
+ do i=1,maxres
+ dyn_ss_mask(i)=.false.
+ enddo
C
C Initialize timing.
C
include 'COMMON.NAMES'
include 'COMMON.FFIELD'
data restyp /
+ &'DD' ,'DPR','DLY','DAR','DHI','DAS','DGL','DSG','DGN','DSN','DTH',
+ &'DYY','DAL','DTY','DTR','DVA','DLE','DIL','DPN','MED','DCY','ZER',
&'CYS','MET','PHE','ILE','LEU','VAL','TRP','TYR','ALA','GLY','THR',
&'SER','GLN','ASN','GLU','ASP','HIS','ARG','LYS','PRO','D'/
data onelet /
+ &'z','p','k','r','h','d','e','n','q','s','t','g',
+ &'a','y','w','v','l','i','f','m','c','x',
&'C','M','F','I','L','V','W','Y','A','G','T',
&'S','Q','N','E','D','H','R','K','P','X'/
data potname /'LJ','LJK','BP','GB','GBV'/
do ii=1,nss
if (ihpb(ii).eq.i+nres) then
scheck=.true.
+ if (dyn_ss) go to 10
jj=jhpb(ii)-nres
goto 10
endif
include 'COMMON.SCCOR'
include 'COMMON.SCROT'
character*1 t1,t2,t3
- character*1 onelett(4) /"G","A","P","D"/
+ character*1 onelett(-2:2) /"p","a","G","A","P"/
logical lprint
dimension blower(3,3,maxlob)
double precision ip,mp
C of the virtual-bond valence angles theta
C
do i=1,ntyp
- read (ithep,*) a0thet(i),(athet(j,i),j=1,2),(bthet(j,i),j=1,2)
+ read (ithep,*) a0thet(i),(athet(j,i,1,1),j=1,2),
+ & (bthet(j,i,1,1),j=1,2)
read (ithep,*) (polthet(j,i),j=0,3)
read (ithep,*) (gthet(j,i),j=1,3)
read (ithep,*) theta0(i),sig0(i),sigc0(i)
sigc0(i)=sigc0(i)**2
enddo
+ do i=1,ntyp
+ athet(1,i,1,-1)=athet(1,i,1,1)
+ athet(2,i,1,-1)=athet(2,i,1,1)
+ bthet(1,i,1,-1)=-bthet(1,i,1,1)
+ bthet(2,i,1,-1)=-bthet(2,i,1,1)
+ athet(1,i,-1,1)=-athet(1,i,1,1)
+ athet(2,i,-1,1)=-athet(2,i,1,1)
+ bthet(1,i,-1,1)=bthet(1,i,1,1)
+ bthet(2,i,-1,1)=bthet(2,i,1,1)
+ enddo
+ do i=-ntyp,-1
+ a0thet(i)=a0thet(-i)
+ athet(1,i,-1,-1)=athet(1,-i,1,1)
+ athet(2,i,-1,-1)=-athet(2,-i,1,1)
+ bthet(1,i,-1,-1)=bthet(1,-i,1,1)
+ bthet(2,i,-1,-1)=-bthet(2,-i,1,1)
+ athet(1,i,-1,1)=athet(1,-i,1,1)
+ athet(2,i,-1,1)=-athet(2,-i,1,1)
+ bthet(1,i,-1,1)=-bthet(1,-i,1,1)
+ bthet(2,i,-1,1)=bthet(2,-i,1,1)
+ athet(1,i,1,-1)=-athet(1,-i,1,1)
+ athet(2,i,1,-1)=athet(2,-i,1,1)
+ bthet(1,i,1,-1)=bthet(1,-i,1,1)
+ bthet(2,i,1,-1)=-bthet(2,-i,1,1)
+ theta0(i)=theta0(-i)
+ sig0(i)=sig0(-i)
+ sigc0(i)=sigc0(-i)
+ do j=0,3
+ polthet(j,i)=polthet(j,-i)
+ enddo
+ do j=1,3
+ gthet(j,i)=gthet(j,-i)
+ enddo
+ enddo
close (ithep)
if (lprint) then
c write (iout,'(a)')
& ' b1*10^1 ',' b2*10^1 '
do i=1,ntyp
write(iout,'(a3,1h&,2x,5(f8.3,1h&))') restyp(i),
- & a0thet(i),(100*athet(j,i),j=1,2),(10*bthet(j,i),j=1,2)
+ & a0thet(i),(100*athet(j,i,1,1),j=1,2),
+ & (10*bthet(j,i,1,1),j=1,2)
enddo
write (iout,'(/a/9x,5a/79(1h-))')
& 'Parameters of the expression for sigma(theta_c):',
& ntheterm3,nsingle,ndouble
nntheterm=max0(ntheterm,ntheterm2,ntheterm3)
read (ithep,*) (ithetyp(i),i=1,ntyp1)
- do i=1,maxthetyp
- do j=1,maxthetyp
- do k=1,maxthetyp
- aa0thet(i,j,k)=0.0d0
+ do i=-ntyp1,-1
+ ithetyp(i)=-ithetyp(-i)
+ enddo
+ do iblock=1,2
+ do i=-maxthetyp,maxthetyp
+ do j=-maxthetyp,maxthetyp
+ do k=-maxthetyp,maxthetyp
+ aa0thet(i,j,k,iblock)=0.0d0
do l=1,ntheterm
- aathet(l,i,j,k)=0.0d0
+ aathet(l,i,j,k,iblock)=0.0d0
enddo
do l=1,ntheterm2
do m=1,nsingle
- bbthet(m,l,i,j,k)=0.0d0
- ccthet(m,l,i,j,k)=0.0d0
- ddthet(m,l,i,j,k)=0.0d0
- eethet(m,l,i,j,k)=0.0d0
+ bbthet(m,l,i,j,k,iblock)=0.0d0
+ ccthet(m,l,i,j,k,iblock)=0.0d0
+ ddthet(m,l,i,j,k,iblock)=0.0d0
+ eethet(m,l,i,j,k,iblock)=0.0d0
enddo
enddo
do l=1,ntheterm3
do m=1,ndouble
do mm=1,ndouble
- ffthet(mm,m,l,i,j,k)=0.0d0
- ggthet(mm,m,l,i,j,k)=0.0d0
+ ffthet(mm,m,l,i,j,k,iblock)=0.0d0
+ ggthet(mm,m,l,i,j,k,iblock)=0.0d0
enddo
enddo
enddo
enddo
enddo
enddo
- do i=1,nthetyp
- do j=1,nthetyp
- do k=1,nthetyp
- read (ithep,'(3a)') res1,res2,res3
- read (ithep,*) aa0thet(i,j,k)
- read (ithep,*)(aathet(l,i,j,k),l=1,ntheterm)
+ enddo
+ do iblock=1,2
+ do i=0,nthetyp
+ do j=-nthetyp,nthetyp
+ do k=-nthetyp,nthetyp
+ read (ithep,'(6a)') res1
+ read (ithep,*) aa0thet(i,j,k,iblock)
+ read (ithep,*)(aathet(l,i,j,k,iblock),l=1,ntheterm)
read (ithep,*)
- & ((bbthet(lll,ll,i,j,k),lll=1,nsingle),
- & (ccthet(lll,ll,i,j,k),lll=1,nsingle),
- & (ddthet(lll,ll,i,j,k),lll=1,nsingle),
- & (eethet(lll,ll,i,j,k),lll=1,nsingle),ll=1,ntheterm2)
+ & ((bbthet(lll,ll,i,j,k,iblock),lll=1,nsingle),
+ & (ccthet(lll,ll,i,j,k,iblock),lll=1,nsingle),
+ & (ddthet(lll,ll,i,j,k,iblock),lll=1,nsingle),
+ & (eethet(lll,ll,i,j,k,iblock),lll=1,nsingle)
+ & ,ll=1,ntheterm2)
read (ithep,*)
- & (((ffthet(llll,lll,ll,i,j,k),ffthet(lll,llll,ll,i,j,k),
- & ggthet(llll,lll,ll,i,j,k),ggthet(lll,llll,ll,i,j,k),
+ & (((ffthet(llll,lll,ll,i,j,k,iblock),
+ & ffthet(lll,llll,ll,i,j,k,iblock),
+ & ggthet(llll,lll,ll,i,j,k,iblock),
+ & ggthet(lll,llll,ll,i,j,k,iblock),
& llll=1,lll-1),lll=2,ndouble),ll=1,ntheterm3)
enddo
enddo
do i=1,nthetyp
do j=1,nthetyp
do l=1,ntheterm
- aathet(l,i,j,nthetyp+1)=aathet(l,i,j,1)
- aathet(l,nthetyp+1,i,j)=aathet(l,1,i,j)
+ aathet(l,i,j,nthetyp+1,iblock)=0.0d0
+ aathet(l,nthetyp+1,i,j,iblock)=0.0d0
enddo
- aa0thet(i,j,nthetyp+1)=aa0thet(i,j,1)
- aa0thet(nthetyp+1,i,j)=aa0thet(1,i,j)
+ aa0thet(i,j,nthetyp+1,iblock)=0.0d0
+ aa0thet(nthetyp+1,i,j,iblock)=0.0d0
enddo
do l=1,ntheterm
- aathet(l,nthetyp+1,i,nthetyp+1)=aathet(l,1,i,1)
+ aathet(l,nthetyp+1,i,nthetyp+1,iblock)=0.0d0
enddo
- aa0thet(nthetyp+1,i,nthetyp+1)=aa0thet(1,i,1)
+ aa0thet(nthetyp+1,i,nthetyp+1,iblock)=0.0d0
enddo
+ enddo
+C Substitution for D aminoacids from symmetry.
+ do iblock=1,2
+ do i=-nthetyp,0
+ do j=-nthetyp,nthetyp
+ do k=-nthetyp,nthetyp
+ aa0thet(i,j,k,iblock)=aa0thet(-i,-j,-k,iblock)
+ do l=1,ntheterm
+ aathet(l,i,j,k,iblock)=aathet(l,-i,-j,-k,iblock)
+ enddo
+ do ll=1,ntheterm2
+ do lll=1,nsingle
+ bbthet(lll,ll,i,j,k,iblock)=bbthet(lll,ll,-i,-j,-k,iblock)
+ ccthet(lll,ll,i,j,k,iblock)=-ccthet(lll,ll,-i,-j,-k,iblock)
+ ddthet(lll,ll,i,j,k,iblock)=ddthet(lll,ll,-i,-j,-k,iblock)
+ eethet(lll,ll,i,j,k,iblock)=-eethet(lll,ll,-i,-j,-k,iblock)
+ enddo
+ enddo
+ do ll=1,ntheterm3
+ do lll=2,ndouble
+ do llll=1,lll-1
+ ffthet(llll,lll,ll,i,j,k,iblock)=
+ & ffthet(llll,lll,ll,-i,-j,-k,iblock)
+ ffthet(lll,llll,ll,i,j,k,iblock)=
+ & ffthet(lll,llll,ll,-i,-j,-k,iblock)
+ ggthet(llll,lll,ll,i,j,k,iblock)=
+ & -ggthet(llll,lll,ll,-i,-j,-k,iblock)
+ ggthet(lll,llll,ll,i,j,k,iblock)=
+ & -ggthet(lll,llll,ll,-i,-j,-k,iblock)
+ enddo !ll
+ enddo !lll
+ enddo !llll
+ enddo !k
+ enddo !j
+ enddo !i
+ enddo !iblock
+
C
C Control printout of the coefficients of virtual-bond-angle potentials
C
write (iout,'(//4a)')
& 'Type ',onelett(i),onelett(j),onelett(k)
write (iout,'(//a,10x,a)') " l","a[l]"
- write (iout,'(i2,1pe15.5)') 0,aa0thet(i,j,k)
+ write (iout,'(i2,1pe15.5)') 0,aa0thet(i,j,k,iblock)
write (iout,'(i2,1pe15.5)')
- & (l,aathet(l,i,j,k),l=1,ntheterm)
+ & (l,aathet(l,i,j,k,iblock),l=1,ntheterm)
do l=1,ntheterm2
write (iout,'(//2h m,4(9x,a,3h[m,i1,1h]))')
& "b",l,"c",l,"d",l,"e",l
do m=1,nsingle
write (iout,'(i2,4(1pe15.5))') m,
- & bbthet(m,l,i,j,k),ccthet(m,l,i,j,k),
- & ddthet(m,l,i,j,k),eethet(m,l,i,j,k)
+ & bbthet(m,l,i,j,k,iblock),ccthet(m,l,i,j,k,iblock),
+ & ddthet(m,l,i,j,k,iblock),eethet(m,l,i,j,k,iblock)
enddo
enddo
do l=1,ntheterm3
do m=2,ndouble
do n=1,m-1
write (iout,'(i1,1x,i1,4(1pe15.5))') n,m,
- & ffthet(n,m,l,i,j,k),ffthet(m,n,l,i,j,k),
- & ggthet(n,m,l,i,j,k),ggthet(m,n,l,i,j,k)
+ & ffthet(n,m,l,i,j,k,iblock),
+ & ffthet(m,n,l,i,j,k,iblock),
+ & ggthet(n,m,l,i,j,k,iblock),
+ & ggthet(m,n,l,i,j,k,iblock)
enddo
enddo
enddo
enddo
bsc(1,i)=0.0D0
read(irotam,*)(censc(k,1,i),k=1,3),((blower(k,l,1),l=1,k),k=1,3)
+ censc(1,1,-i)=censc(1,1,i)
+ censc(2,1,-i)=censc(2,1,i)
+ censc(3,1,-i)=-censc(3,1,i)
do j=2,nlob(i)
read (irotam,*) bsc(j,i)
read (irotam,*) (censc(k,j,i),k=1,3),
& ((blower(k,l,j),l=1,k),k=1,3)
+ censc(1,j,-i)=censc(1,j,i)
+ censc(2,j,-i)=censc(2,j,i)
+ censc(3,j,-i)=-censc(3,j,i)
+C BSC is amplitude of Gaussian
enddo
do j=1,nlob(i)
do k=1,3
enddo
gaussc(k,l,j,i)=akl
gaussc(l,k,j,i)=akl
+ if (((k.eq.3).and.(l.ne.3))
+ & .or.((l.eq.3).and.(k.ne.3))) then
+ gaussc(k,l,j,-i)=-akl
+ gaussc(l,k,j,-i)=-akl
+ else
+ gaussc(k,l,j,-i)=akl
+ gaussc(l,k,j,-i)=akl
+ endif
enddo
enddo
enddo
read (itorp,*) ntortyp
read (itorp,*) (itortyp(i),i=1,ntyp)
write (iout,*) 'ntortyp',ntortyp
- do i=1,ntortyp
- do j=1,ntortyp
- read (itorp,*) nterm(i,j),nlor(i,j)
+ do iblock=1,2
+ do i=-ntyp,-1
+ itortyp(i)=-itortyp(-i)
+ enddo
+c write (iout,*) 'ntortyp',ntortyp
+ do i=0,ntortyp-1
+ do j=-ntortyp+1,ntortyp-1
+ read (itorp,*) nterm(i,j,iblock),
+ & nlor(i,j,iblock)
+ nterm(-i,-j,iblock)=nterm(i,j,iblock)
+ nlor(-i,-j,iblock)=nlor(i,j,iblock)
v0ij=0.0d0
si=-1.0d0
- do k=1,nterm(i,j)
- read (itorp,*) kk,v1(k,i,j),v2(k,i,j)
- v0ij=v0ij+si*v1(k,i,j)
+ do k=1,nterm(i,j,iblock)
+ read (itorp,*) kk,v1(k,i,j,iblock),
+ & v2(k,i,j,iblock)
+ v1(k,-i,-j,iblock)=v1(k,i,j,iblock)
+ v2(k,-i,-j,iblock)=-v2(k,i,j,iblock)
+ v0ij=v0ij+si*v1(k,i,j,iblock)
si=-si
enddo
- do k=1,nlor(i,j)
- read (itorp,*) kk,vlor1(k,i,j),vlor2(k,i,j),vlor3(k,i,j)
+ do k=1,nlor(i,j,iblock)
+ read (itorp,*) kk,vlor1(k,i,j),
+ & vlor2(k,i,j),vlor3(k,i,j)
v0ij=v0ij+vlor1(k,i,j)/(1+vlor3(k,i,j)**2)
enddo
- v0(i,j)=v0ij
+ v0(i,j,iblock)=v0ij
+ v0(-i,-j,iblock)=v0ij
enddo
enddo
+ enddo
close (itorp)
if (lprint) then
write (iout,'(/a/)') 'Torsional constants:'
do j=1,ntortyp
write (iout,*) 'ityp',i,' jtyp',j
write (iout,*) 'Fourier constants'
- do k=1,nterm(i,j)
- write (iout,'(2(1pe15.5))') v1(k,i,j),v2(k,i,j)
+ do k=1,nterm(i,j,iblock)
+ write (iout,'(2(1pe15.5))') v1(k,i,j,iblock),
+ & v2(k,i,j,iblock)
enddo
write (iout,*) 'Lorenz constants'
- do k=1,nlor(i,j)
+ do k=1,nlor(i,j,iblock)
write (iout,'(3(1pe15.5))')
& vlor1(k,i,j),vlor2(k,i,j),vlor3(k,i,j)
enddo
C
C 6/23/01 Read parameters for double torsionals
C
- do i=1,ntortyp
- do j=1,ntortyp
- do k=1,ntortyp
+ do iblock=1,2
+ do i=0,ntortyp-1
+ do j=-ntortyp+1,ntortyp-1
+ do k=-ntortyp+1,ntortyp-1
read (itordp,'(3a1)') t1,t2,t3
if (t1.ne.onelett(i) .or. t2.ne.onelett(j)
& .or. t3.ne.onelett(k)) then
& i,j,k,t1,t2,t3
stop "Error in double torsional parameter file"
endif
- read (itordp,*) ntermd_1(i,j,k),ntermd_2(i,j,k)
- read (itordp,*) (v1c(1,l,i,j,k),l=1,ntermd_1(i,j,k))
- read (itordp,*) (v1s(1,l,i,j,k),l=1,ntermd_1(i,j,k))
- read (itordp,*) (v1c(2,l,i,j,k),l=1,ntermd_1(i,j,k))
- read (itordp,*) (v1s(2,l,i,j,k),l=1,ntermd_1(i,j,k))
- read (itordp,*) ((v2c(l,m,i,j,k),v2c(m,l,i,j,k),
- & v2s(l,m,i,j,k),v2s(m,l,i,j,k),m=1,l-1),l=1,ntermd_2(i,j,k))
- enddo
- enddo
- enddo
+ read (itordp,*) ntermd_1(i,j,k,iblock),
+ & ntermd_2(i,j,k,iblock)
+ ntermd_1(-i,-j,-k,iblock)=ntermd_1(i,j,k,iblock)
+ ntermd_2(-i,-j,-k,iblock)=ntermd_2(i,j,k,iblock)
+ read (itordp,*) (v1c(1,l,i,j,k,iblock),l=1,
+ & ntermd_1(i,j,k,iblock))
+ read (itordp,*) (v1s(1,l,i,j,k,iblock),l=1,
+ & ntermd_1(i,j,k,iblock))
+ read (itordp,*) (v1c(2,l,i,j,k,iblock),l=1,
+ & ntermd_1(i,j,k,iblock))
+ read (itordp,*) (v1s(2,l,i,j,k,iblock),l=1,
+ & ntermd_1(i,j,k,iblock))
+C Martix of D parameters for one dimesional foureir series
+ do l=1,ntermd_1(i,j,k,iblock)
+ v1c(1,l,-i,-j,-k,iblock)=v1c(1,l,i,j,k,iblock)
+ v1s(1,l,-i,-j,-k,iblock)=-v1s(1,l,i,j,k,iblock)
+ v1c(2,l,-i,-j,-k,iblock)=v1c(2,l,i,j,k,iblock)
+ v1s(2,l,-i,-j,-k,iblock)=-v1s(2,l,i,j,k,iblock)
+c write(iout,*) "whcodze" ,
+c & v1s(2,l,-i,-j,-k,iblock),v1s(2,l,i,j,k,iblock)
+ enddo
+ read (itordp,*) ((v2c(l,m,i,j,k,iblock),
+ & v2c(m,l,i,j,k,iblock),v2s(l,m,i,j,k,iblock),
+ & v2s(m,l,i,j,k,iblock),
+ & m=1,l-1),l=1,ntermd_2(i,j,k,iblock))
+C Martix of D parameters for two dimesional fourier series
+ do l=1,ntermd_2(i,j,k,iblock)
+ do m=1,l-1
+ v2c(l,m,-i,-j,-k,iblock)=v2c(l,m,i,j,k,iblock)
+ v2c(m,l,-i,-j,-k,iblock)=v2c(m,l,i,j,k,iblock)
+ v2s(l,m,-i,-j,-k,iblock)=-v2s(l,m,i,j,k,iblock)
+ v2s(m,l,-i,-j,-k,iblock)=-v2s(m,l,i,j,k,iblock)
+ enddo!m
+ enddo!l
+ enddo!k
+ enddo!j
+ enddo!i
+ enddo!iblock
if (lprint) then
write (iout,*)
write (iout,*) 'Constants for double torsionals'
- do i=1,ntortyp
- do j=1,ntortyp
- do k=1,ntortyp
+ do iblock=1,2
+ do i=0,ntortyp-1
+ do j=-ntortyp+1,ntortyp-1
+ do k=-ntortyp+1,ntortyp-1
write (iout,*) 'ityp',i,' jtyp',j,' ktyp',k,
- & ' nsingle',ntermd_1(i,j,k),' ndouble',ntermd_2(i,j,k)
+ & ' nsingle',ntermd_1(i,j,k,iblock),
+ & ' ndouble',ntermd_2(i,j,k,iblock)
write (iout,*)
write (iout,*) 'Single angles:'
- do l=1,ntermd_1(i,j,k)
- write (iout,'(i5,2f10.5,5x,2f10.5)') l,
- & v1c(1,l,i,j,k),v1s(1,l,i,j,k),
- & v1c(2,l,i,j,k),v1s(2,l,i,j,k)
+ do l=1,ntermd_1(i,j,k,iblock)
+ write (iout,'(i5,2f10.5,5x,2f10.5,5x,2f10.5)') l,
+ & v1c(1,l,i,j,k,iblock),v1s(1,l,i,j,k,iblock),
+ & v1c(2,l,i,j,k,iblock),v1s(2,l,i,j,k,iblock),
+ & v1s(1,l,-i,-j,-k,iblock),v1s(2,l,-i,-j,-k,iblock)
enddo
write (iout,*)
write (iout,*) 'Pairs of angles:'
- write (iout,'(3x,20i10)') (l,l=1,ntermd_2(i,j,k))
- do l=1,ntermd_2(i,j,k)
- write (iout,'(i5,20f10.5)')
- & l,(v2c(l,m,i,j,k),m=1,ntermd_2(i,j,k))
+ write (iout,'(3x,20i10)') (l,l=1,ntermd_2(i,j,k,iblock))
+ do l=1,ntermd_2(i,j,k,iblock)
+ write (iout,'(i5,20f10.5)')
+ & l,(v2c(l,m,i,j,k,iblock),m=1,ntermd_2(i,j,k,iblock))
enddo
write (iout,*)
- write (iout,'(3x,20i10)') (l,l=1,ntermd_2(i,j,k))
- do l=1,ntermd_2(i,j,k)
- write (iout,'(i5,20f10.5)')
- & l,(v2s(l,m,i,j,k),m=1,ntermd_2(i,j,k))
+ write (iout,'(3x,20i10)') (l,l=1,ntermd_2(i,j,k,iblock))
+ do l=1,ntermd_2(i,j,k,iblock)
+ write (iout,'(i5,20f10.5)')
+ & l,(v2s(l,m,i,j,k,iblock),m=1,ntermd_2(i,j,k,iblock)),
+ & (v2s(l,m,-i,-j,-k,iblock),m=1,ntermd_2(i,j,k,iblock))
enddo
write (iout,*)
enddo
enddo
enddo
+ enddo
endif
#endif
C Read of Side-chain backbone correlation parameters
read (isccor,*) nsccortyp
read (isccor,*) (isccortyp(i),i=1,ntyp)
c write (iout,*) 'ntortyp',ntortyp
+ do i=-ntyp,-1
+ isccortyp(i)=-isccortyp(-i)
+ enddo
+ iscprol=isccortyp(20)
maxinter=3
cc maxinter is maximum interaction sites
do l=1,maxinter
read (isccor,*)
&nterm_sccor(i,j),nlor_sccor(i,j)
v0ijsccor=0.0d0
- si=-1.0d0
-
+ v0ijsccor1=0.0d0
+ v0ijsccor2=0.0d0
+ v0ijsccor3=0.0d0
+ si=-1.0d0
+ nterm_sccor(-i,j)=nterm_sccor(i,j)
+ nterm_sccor(-i,-j)=nterm_sccor(i,j)
+ nterm_sccor(i,-j)=nterm_sccor(i,j)
do k=1,nterm_sccor(i,j)
read (isccor,*) kk,v1sccor(k,l,i,j)
& ,v2sccor(k,l,i,j)
+ if (j.eq.iscprol) then
+ if (i.eq.isccortyp(10)) then
+ v1sccor(k,l,i,-j)=v1sccor(k,l,i,j)
+ v2sccor(k,l,i,-j)=-v2sccor(k,l,i,j)
+ else
+ v1sccor(k,l,i,-j)=v1sccor(k,l,i,j)*0.5d0
+ & +v2sccor(k,l,i,j)*dsqrt(0.75d0)
+ v2sccor(k,l,i,-j)=-v2sccor(k,l,i,j)*0.5d0
+ & +v1sccor(k,l,i,j)*dsqrt(0.75d0)
+ v1sccor(k,l,-i,-j)=v1sccor(k,l,i,j)
+ v2sccor(k,l,-i,-j)=-v2sccor(k,l,i,j)
+ v1sccor(k,l,-i,j)=v1sccor(k,l,i,-j)
+ v2sccor(k,l,-i,j)=-v2sccor(k,l,i,-j)
+ endif
+ else
+ if (i.eq.isccortyp(10)) then
+ v1sccor(k,l,i,-j)=v1sccor(k,l,i,j)
+ v2sccor(k,l,i,-j)=-v2sccor(k,l,i,j)
+ else
+ if (j.eq.isccortyp(10)) then
+ v1sccor(k,l,-i,j)=v1sccor(k,l,i,j)
+ v2sccor(k,l,-i,j)=-v2sccor(k,l,i,j)
+ else
+ v1sccor(k,l,i,-j)=-v1sccor(k,l,i,j)
+ v2sccor(k,l,i,-j)=-v2sccor(k,l,i,j)
+ v1sccor(k,l,-i,-j)=v1sccor(k,l,i,j)
+ v2sccor(k,l,-i,-j)=-v2sccor(k,l,i,j)
+ v1sccor(k,l,-i,j)=v1sccor(k,l,i,-j)
+ v2sccor(k,l,-i,j)=-v2sccor(k,l,i,-j)
+ endif
+ endif
+ endif
v0ijsccor=v0ijsccor+si*v1sccor(k,l,i,j)
+ v0ijsccor1=v0ijsccor+si*v1sccor(k,l,-i,j)
+ v0ijsccor2=v0ijsccor+si*v1sccor(k,l,i,-j)
+ v0ijsccor3=v0ijsccor+si*v1sccor(k,l,-i,-j)
si=-si
enddo
do k=1,nlor_sccor(i,j)
v0ijsccor=v0ijsccor+vlor1sccor(k,i,j)/
&(1+vlor3sccor(k,i,j)**2)
enddo
- v0sccor(i,j)=v0ijsccor
+ v0sccor(l,i,j)=v0ijsccor
+ v0sccor(l,-i,j)=v0ijsccor1
+ v0sccor(l,i,-j)=v0ijsccor2
+ v0sccor(l,-i,-j)=v0ijsccor3
enddo
enddo
enddo
C interaction energy of the Gly, Ala, and Pro prototypes.
C
read (ifourier,*) nloctyp
- do i=1,nloctyp
+ do i=0,nloctyp-1
read (ifourier,*)
read (ifourier,*) (b(ii,i),ii=1,13)
if (lprint) then
endif
B1(1,i) = b(3,i)
B1(2,i) = b(5,i)
+ B1(1,-i) = b(3,i)
+ B1(2,-i) = -b(5,i)
B1tilde(1,i) = b(3,i)
B1tilde(2,i) =-b(5,i)
+ B1tilde(1,-i) =-b(3,i)
+ B1tilde(2,-i) =b(5,i)
B2(1,i) = b(2,i)
B2(2,i) = b(4,i)
+ B2(1,-i) =b(2,i)
+ B2(2,-i) =-b(4,i)
CC(1,1,i)= b(7,i)
CC(2,2,i)=-b(7,i)
CC(2,1,i)= b(9,i)
CC(1,2,i)= b(9,i)
+ CC(1,1,-i)= b(7,i)
+ CC(2,2,-i)=-b(7,i)
+ CC(2,1,-i)=-b(9,i)
+ CC(1,2,-i)=-b(9,i)
Ctilde(1,1,i)=b(7,i)
Ctilde(1,2,i)=b(9,i)
Ctilde(2,1,i)=-b(9,i)
Ctilde(2,2,i)=b(7,i)
+ Ctilde(1,1,-i)=b(7,i)
+ Ctilde(1,2,-i)=-b(9,i)
+ Ctilde(2,1,-i)=b(9,i)
+ Ctilde(2,2,-i)=b(7,i)
DD(1,1,i)= b(6,i)
DD(2,2,i)=-b(6,i)
DD(2,1,i)= b(8,i)
DD(1,2,i)= b(8,i)
+ DD(1,1,-i)= b(6,i)
+ DD(2,2,-i)=-b(6,i)
+ DD(2,1,-i)=-b(8,i)
+ DD(1,2,-i)=-b(8,i)
Dtilde(1,1,i)=b(6,i)
Dtilde(1,2,i)=b(8,i)
Dtilde(2,1,i)=-b(8,i)
Dtilde(2,2,i)=b(6,i)
+ Dtilde(1,1,-i)=b(6,i)
+ Dtilde(1,2,-i)=-b(8,i)
+ Dtilde(2,1,-i)=b(8,i)
+ Dtilde(2,2,-i)=b(6,i)
EE(1,1,i)= b(10,i)+b(11,i)
EE(2,2,i)=-b(10,i)+b(11,i)
EE(2,1,i)= b(12,i)-b(13,i)
EE(1,2,i)= b(12,i)+b(13,i)
+ EE(1,1,-i)= b(10,i)+b(11,i)
+ EE(2,2,-i)=-b(10,i)+b(11,i)
+ EE(2,1,-i)=-b(12,i)+b(13,i)
+ EE(1,2,-i)=-b(12,i)-b(13,i)
enddo
if (lprint) then
do i=1,nloctyp
C
C Define the constants of the disulfide bridge
C
- ebr=-5.50D0
+ C ebr=-5.50D0
c
c Old arbitrary potential - commented out.
c
c energy surface of diethyl disulfide.
c A. Liwo and U. Kozlowska, 11/24/03
c
- D0CM = 3.78d0
- AKCM = 15.1d0
- AKTH = 11.0d0
- AKCT = 12.0d0
- V1SS =-1.08d0
- V2SS = 7.61d0
- V3SS = 13.7d0
-
- write (iout,'(/a)') "Disulfide bridge parameters:"
- write (iout,'(a,f10.2)') 'S-S bridge energy: ',ebr
- write (iout,'(2(a,f10.2))') 'd0cm:',d0cm,' akcm:',akcm
- write (iout,'(2(a,f10.2))') 'akth:',akth,' akct:',akct
- write (iout,'(3(a,f10.2))') 'v1ss:',v1ss,' v2ss:',v2ss,
- & ' v3ss:',v3ss
+ C D0CM = 3.78d0
+ C AKCM = 15.1d0
+ C AKTH = 11.0d0
+ C AKCT = 12.0d0
+ C V1SS =-1.08d0
+ C V2SS = 7.61d0
+ C V3SS = 13.7d0
return
end
call xdrfint_(ixdrf, nss, iret)
if (iret.eq.0) goto 101
do j=1,nss
- call xdrfint_(ixdrf, ihpb(j), iret)
- if (iret.eq.0) goto 101
- call xdrfint_(ixdrf, jhpb(j), iret)
- if (iret.eq.0) goto 101
+ cc if (dyn_ss) then
+ cc call xdrfint_(ixdrf, idssb(j), iret)
+ cc if (iret.eq.0) goto 101
+ cc call xdrfint_(ixdrf, jdssb(j), iret)
+ cc if (iret.eq.0) goto 101
+ cc idssb(j)=idssb(j)-nres
+ cc jdssb(j)=jdssb(j)-nres
+ cc else
+ call xdrfint_(ixdrf, ihpb(j), iret)
+ if (iret.eq.0) goto 101
+ call xdrfint_(ixdrf, jhpb(j), iret)
+ if (iret.eq.0) goto 101
+ cc endif
enddo
call xdrffloat_(ixdrf,reini,iret)
if (iret.eq.0) goto 101
call flush(iout)
if (iret.eq.0) goto 101
do k=1,nss
- call xdrfint(ixdrf, ihpb(k), iret)
- if (iret.eq.0) goto 101
- call xdrfint(ixdrf, jhpb(k), iret)
- if (iret.eq.0) goto 101
+ cc if (dyn_ss) then
+ cc call xdrfint(ixdrf, idssb(k), iret)
+ cc if (iret.eq.0) goto 101
+ cc call xdrfint(ixdrf, jdssb(k), iret)
+ cc if (iret.eq.0) goto 101
+ cc idssb(k)=idssb(k)-nres
+ cc jdssb(k)=jdssb(k)-nres
+ cc write(iout,*) "TUTU", idssb(k),jdssb(k)
+ cc else
+ call xdrfint(ixdrf, ihpb(k), iret)
+ if (iret.eq.0) goto 101
+ call xdrfint(ixdrf, jhpb(k), iret)
+ if (iret.eq.0) goto 101
+ cc endif
enddo
call xdrffloat(ixdrf,reini,iret)
if (iret.eq.0) goto 101
if (iret.eq.0) goto 101
#endif
energy(jj+1)=reini
- entfac(jj+1)=refree
+ cc write(iout,*) 'reini=', reini, jj+1
+ entfac(jj+1)=dble(refree)
+ cc write(iout,*) 'refree=', refree,jj+1
rmstb(jj+1)=rmsdev
do k=1,nres
do l=1,3
enddo
do j=nnt,nct
itj=itype(j)
- if (itype(j).ne.10 .and. (vbld(nres+j)-dsc(itj)).gt.2.0d0) then
+ if (itype(j).ne.10 .and. (vbld(nres+j)-dsc(iabs(itj))).gt.2.0d0)
+ & then
write (iout,*) "Conformation",jjj,jj+1
write (iout,*) "Bad CA-SC bond length",j," ",vbld(nres+j)
write (iout,*) "The Cartesian geometry is:"
write (iout,*) "Reading binary file, record",iii," ii",ii
call flush(iout)
#endif
+ if (dyn_ss) then
+ read(icbase,rec=iii) ((allcart(j,i,ij),j=1,3),i=1,nres),
+ & ((allcart(j,i,ij),j=1,3),i=nnt+nres,nct+nres),
+ c & nss_all(ij),(ihpb_all(i,ij),jhpb_all(i,ij),i=1,nss),
+ & entfac(ii),rmstb(ii)
+ else
read(icbase,rec=iii) ((allcart(j,i,ij),j=1,3),i=1,nres),
& ((allcart(j,i,ij),j=1,3),i=nnt+nres,nct+nres),
& nss_all(ij),(ihpb_all(i,ij),jhpb_all(i,ij),i=1,nss),
& entfac(ii),rmstb(ii)
+ endif
#ifdef DEBUG
write (iout,*) ii,iii,ij,entfac(ii)
write (iout,'(8f10.5)') ((allcart(j,i,ij),j=1,3),i=1,nres)
write (iout,*) "Writing binary file, record",iii," ii",ii
call flush(iout)
#endif
+ if (dyn_ss) then
+ write(unit_out,rec=iii) ((allcart(j,i,ij),j=1,3),i=1,nres),
+ & ((allcart(j,i,ij),j=1,3),i=nnt+nres,nct+nres),
+ c & nss_all(ij),(ihpb_all(i,ij),jhpb_all(i,ij),i=1,nss_all(ij))
+ & entfac(ii),rmstb(ii)
+ else
write(unit_out,rec=iii) ((allcart(j,i,ij),j=1,3),i=1,nres),
& ((allcart(j,i,ij),j=1,3),i=nnt+nres,nct+nres),
& nss_all(ij),(ihpb_all(i,ij),jhpb_all(i,ij),i=1,nss_all(ij)),
& entfac(ii),rmstb(ii)
+ endif
#ifdef DEBUG
write (iout,'(8f10.5)') ((allcart(j,i,ij),j=1,3),i=1,nres)
write (iout,'(8f10.4)') ((allcart(j,i,ij),j=1,3),i=nnt+nres,
refstr=(index(controlcard,'REFSTR').gt.0)
write (iout,*) "REFSTR",refstr
pdbref=(index(controlcard,'PDBREF').gt.0)
+ dyn_ss=(index(controlcard,'DYN_SS').gt.0)
iscode=index(controlcard,'ONE_LETTER')
tree=(index(controlcard,'MAKE_TREE').gt.0)
min_var=(index(controlcard,'MINVAR').gt.0)
call reada(weightcard,'SCALSCP',scalscp,1.0d0)
call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0)
call reada(weightcard,'DELT_CORR',delt_corr,0.5d0)
+ call reada(weightcard,'WSCCOR',wsccor,1.0D0)
+ call reada(weightcard,"D0CM",d0cm,3.78d0)
+ call reada(weightcard,"AKCM",akcm,15.1d0)
+ call reada(weightcard,"AKTH",akth,11.0d0)
+ call reada(weightcard,"AKCT",akct,12.0d0)
+ call reada(weightcard,"V1SS",v1ss,-1.08d0)
+ call reada(weightcard,"V2SS",v2ss,7.61d0)
+ call reada(weightcard,"V3SS",v3ss,13.7d0)
+ call reada(weightcard,"EBR",ebr,-5.50D0)
if (index(weightcard,'SOFT').gt.0) ipot=6
C 12/1/95 Added weight for the multi-body term WCORR
call reada(weightcard,'WCORRH',wcorr,1.0D0)
+ do i=1,maxres-1
+ do j=i+1,maxres
+ dyn_ssbond_ij(i,j)=1.0d300
+ enddo
+ enddo
+ call reada(weightcard,"HT",Ht,0.0D0)
+ if (dyn_ss) then
+ ss_depth=ebr/wsc-0.25*eps(1,1)
+ Ht=Ht/wsc-0.25*eps(1,1)
+ akcm=akcm*wstrain/wsc
+ akth=akth*wstrain/wsc
+ akct=akct*wstrain/wsc
+ v1ss=v1ss*wstrain/wsc
+ v2ss=v2ss*wstrain/wsc
+ v3ss=v3ss*wstrain/wsc
+ else
+ ss_depth=ebr/wstrain-0.25*eps(1,1)*wsc/wstrain
+ endif
+ write (iout,'(/a)') "Disulfide bridge parameters:"
+ write (iout,'(a,f10.2)') 'S-S bridge energy: ',ebr
+ write (iout,'(a,f10.2)') 'S-S depth: ',ss_depth
+ write (iout,'(2(a,f10.2))') 'd0cm:',d0cm,' akcm:',akcm
+ write (iout,'(2(a,f10.2))') 'akth:',akth,' akct:',akct
+ write (iout,'(3(a,f10.2))') 'v1ss:',v1ss,' v2ss:',v2ss,
+ & ' v3ss:',v3ss
+ write (iout,'(2(a,f10.2))') 'ht:',ht,' eps:', eps(1,1)
if (wcorr4.gt.0.0d0) wcorr=wcorr4
weights(1)=wsc
weights(2)=wscp
weights(18)=scal14
write (iout,10) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor,
& wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wturn3,
- & wturn4,wturn6
+ & wturn4,wturn6,wsccor
10 format (/'Energy-term weights (unscaled):'//
& 'WSCC= ',f10.6,' (SC-SC)'/
& 'WSCP= ',f10.6,' (SC-p)'/
& 'WCORR6= ',f10.6,' (multi-body 6th order)'/
& 'WTURN3= ',f10.6,' (turns, 3rd order)'/
& 'WTURN4= ',f10.6,' (turns, 4th order)'/
- & 'WTURN6= ',f10.6,' (turns, 6th order)')
+ & 'WTURN6= ',f10.6,' (turns, 6th order)'/
+ & 'WSCCOR= ',f10.6,' (SC-backbone torsinal correalations)')
if (wcorr4.gt.0.0d0) then
write (iout,'(/2a/)') 'Local-electrostatic type correlation ',
& 'between contact pairs of peptide groups'
do i=1,nres
#ifdef PROCOR
- if (itype(i).eq.21 .or. itype(i+1).eq.21) then
+ if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) then
#else
- if (itype(i).eq.21) then
+ if (itype(i).eq.ntyp1) then
#endif
itel(i)=0
#ifdef PROCOR
- else if (itype(i+1).ne.20) then
+ else if (iabs(itype(i+1)).ne.20) then
#else
- else if (itype(i).ne.20) then
+ else if (iabs(itype(i)).ne.20) then
#endif
itel(i)=1
else
nnt=1
nct=nres
print *,'NNT=',NNT,' NCT=',NCT
- if (itype(1).eq.21) nnt=2
- if (itype(nres).eq.21) nct=nct-1
+ if (itype(1).eq.ntyp1) nnt=2
+ if (itype(nres).eq.ntyp1) nct=nct-1
if (nstart.lt.nnt) nstart=nnt
if (nend.gt.nct .or. nend.eq.0) nend=nct
write (iout,*) "nstart",nstart," nend",nend
enddo
endif
endif
+ if (ns.gt.0.and.dyn_ss) then
+ do i=nss+1,nhpb
+ ihpb(i-nss)=ihpb(i)
+ jhpb(i-nss)=jhpb(i)
+ forcon(i-nss)=forcon(i)
+ dhpb(i-nss)=dhpb(i)
+ enddo
+ nhpb=nhpb-nss
+ nss=0
+ call hpb_partition
+ do i=1,ns
+ dyn_ss_mask(iss(i))=.true.
+ c write(iout,*) i,iss(i),dyn_ss_mask(iss(i)),"ATU"
+ enddo
+ endif
+ print *, "Leaving brigde read"
return
end
c----------------------------------------------------------------------------
if (Fortran_COMPILER_NAME STREQUAL "ifort")
set(UNRES_MDM_SRC0 ${UNRES_MDM_SRC0} prng.f )
+ elseif(Fortran_COMPILER_NAME STREQUAL "mpif90")
+ set(UNRES_MDM_SRC0 ${UNRES_MDM_SRC0} prng.f )
else()
set(UNRES_MDM_SRC0 ${UNRES_MDM_SRC0} prng_32.F )
endif (Fortran_COMPILER_NAME STREQUAL "ifort")
set(FFLAGS0 "-ip -w" )
set(FFLAGS1 "-w -g -d2 -CA -CB" )
set(FFLAGS2 "-w -g -00 ")
- #set(FFLAGS3 "-c -w -O3 -ipo -ipo_obj -opt_report" )
set(FFLAGS3 "-w -ipo " )
elseif (Fortran_COMPILER_NAME STREQUAL "gfortran")
- set(FFLAGS0 "-I. " )
- set(FFLAGS1 "-g -I. " )
- set(FFLAGS2 "-I. ")
- #set(FFLAGS3 "-c -w -O3 -ipo -ipo_obj -opt_report" )
- set(FFLAGS3 "-I. " )
+ set(FFLAGS0 "-std=legacy -I. " )
+ set(FFLAGS1 "-std=legacy -g -I. " )
+ set(FFLAGS2 "-std=legacy -I. ")
+ set(FFLAGS3 "-std=legacy -I. " )
endif (Fortran_COMPILER_NAME STREQUAL "ifort")
#=========================================
if(UNRES_MD_FF STREQUAL "GAB" )
# set preprocesor flags
- set(CPPFLAGS "PROCOR -DUNRES -DISNAN -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC" )
+ set(CPPFLAGS "PROCOR -DUNRES -DISNAN -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DSCCORPDB" )
#=========================================
# Settings for E0LL2Y force field
#=========================================
elseif(UNRES_MD_FF STREQUAL "E0LL2Y")
# set preprocesor flags
- set(CPPFLAGS "PROCOR -DUNRES -DISNAN -DSPLITELE -DLANG0" )
+ set(CPPFLAGS "PROCOR -DUNRES -DISNAN -DSPLITELE -DLANG0 -DSCCORPDB" )
endif(UNRES_MD_FF STREQUAL "GAB")
elseif (Fortran_COMPILER_NAME STREQUAL "gfortran")
# Add old gfortran flags
set(CPPFLAGS "${CPPFLAGS} -DG77")
+ else (Fortran_COMPILER_NAME STREQUAL "ifort")
+ # Default preprocessor flags
+ set(CPPFLAGS "${CPPFLAGS} -DPGI")
endif (Fortran_COMPILER_NAME STREQUAL "ifort")
endif(UNRES_WITH_MPI)
#=========================================
- # cinfo.f stupid workaround for cmake
- # - shame on me ]:)
+ # cinfo.f workaround for cmake
#=========================================
- set_property(SOURCE compinfo.c PROPERTY CMAKE_C_FLAGS "-c" )
- add_executable(compinfo-mdm compinfo.c)
- set_target_properties(compinfo-mdm PROPERTIES OUTPUT_NAME compinfo)
-
- set(UNRES_CINFO_DIR "${CMAKE_CURRENT_BINARY_DIR}" )
- add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/cinfo.f
- COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/cinfo.f ${CMAKE_CURRENT_BINARY_DIR}/cinfo.f
- COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/COMMON.IOUNITS ${CMAKE_CURRENT_BINARY_DIR}/COMMON.IOUNITS
- COMMAND ${CMAKE_CURRENT_BINARY_DIR}/compinfo | true
- DEPENDS compinfo-mdm )
- set_property(SOURCE ${UNRES_CINFO_DIR}/cinfo.f PROPERTY COMPILE_FLAGS ${FFLAGS0} )
+ # get the current date
+ TODAY(DATE)
+ # generate cinfo.f
+ set(CINFO "${CMAKE_CURRENT_BINARY_DIR}/cinfo.f")
+ FILE(WRITE ${CINFO}
+ "C CMake generated file
+ subroutine cinfo
+ include 'COMMON.IOUNITS'
+ write(iout,*)'++++ Compile info ++++'
+ write(iout,*)'Version ${UNRES_MAJOR}.${UNRES_MINOR} build ${UNRES_PATCH}'
+ ")
+
+ CINFO_FORMAT(${CINFO} "Compiled" "${DATE}" )
+ CINFO_FORMAT(${CINFO} "Compiled by" "$ENV{USER}@$ENV{HOST}" )
+ CINFO_FORMAT(${CINFO} "OS name:" "${CMAKE_SYSTEM_NAME}" )
+ CINFO_FORMAT(${CINFO} "OS release:" "${CMAKE_SYSTEM}" )
+ CINFO_FORMAT(${CINFO} "Fortran Compiler:" "${CMAKE_Fortran_COMPILER}" )
+ CINFO_FORMAT(${CINFO} "MD Force field:" "${UNRES_MD_FF}" )
+ CINFO_FORMAT(${CINFO} "CPPFLAGS =" "${CPPFLAGS}")
+
+ FILE(APPEND ${CINFO}
+ " write(iout,*)'++++ End of compile info ++++'
+ return
+ end ")
+
+
+ # add include path
+ set_property(SOURCE ${CMAKE_CURRENT_BINARY_DIR}/cinfo.f PROPERTY COMPILE_FLAGS "${FFLAGS0} -I${CMAKE_CURRENT_SOURCE_DIR}")
#=========================================
# Set full unres MD-M sources
#=========================================
- set(UNRES_MDM_SRCS ${UNRES_MDM_SRC0} ${UNRES_MDM_SRC3} ${UNRES_CINFO_DIR}/cinfo.f proc_proc.c )
+ set(UNRES_MDM_SRCS ${UNRES_MDM_SRC0} ${UNRES_MDM_SRC3} ${CMAKE_CURRENT_BINARY_DIR}/cinfo.f proc_proc.c )
#=========================================
# Build the binary
integer nres,nsup,nstart_sup,nz_start,nz_end,iz_sc,
& nres0,nstart_seq,chain_length,iprzes,tabperm,nperm
double precision c,dc,dc_old,d_c_work,xloc,xrot,dc_norm,t,r,
- & prod,rt,dc_work,cref,crefjlee,chain_rep
+ & prod,rt,dc_work,cref,crefjlee,chain_rep,dc_norm2
common /chain/ c(3,maxres2+2),dc(3,0:maxres2),dc_old(3,0:maxres2),
& xloc(3,maxres),xrot(3,maxres),dc_norm(3,0:maxres2),
+ & dc_norm2(3,0:maxres2),
& dc_work(MAXRES6),nres,nres0
common /rotmat/ t(3,3,maxres),r(3,3,maxres),prod(3,3,maxres),
& rt(3,3,maxres)
common /refstruct/ cref(3,maxres2+2,maxperm),
- &crefjlee(3,maxres2+2),
- & nsup,nstart_sup,nstart_seq,chain_rep(3,maxres2+2,maxsym),
+ & crefjlee(3,maxres2+2),
+ & chain_rep(3,maxres2+2,maxsym),
+ & nsup,nstart_sup,nstart_seq,
& chain_length,iprzes,tabperm(maxperm,maxsym),nperm
common /from_zscore/ nz_start,nz_end,iz_sc
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
do j=1,3
ind=ind+1
v_work(ind)=d_t(j,i+nres)
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
inres=i+nres
do j=1,3
d_t(j,inres)=d_t(j,inres)+0.5d0*d_a(j,inres)*d_time
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
inres=i+nres
do j=1,3
adt=d_a_old(j,inres)*d_time
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
inres=i+nres
do j=1,3
d_t(j,inres)=d_t_new(j,inres)+0.5d0*d_a(j,inres)*d_time
ind=ind+3
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
inres=i+nres
do j=1,3
adt=(d_a_old(j,inres)+d_af_work(ind+j))*d_time
ind=ind+3
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
inres=i+nres
do j=1,3
d_t(j,inres)=d_t_new(j,inres)+(0.5d0*(d_a(j,inres)
c if (dabs(accel(j)).gt.amax) amax=dabs(accel(j))
if (dabs(accel(j)).gt.dabs(accel_old(j))) then
dacc=dabs(accel(j)-accel_old(j))
+c write (iout,*) i,dacc
if (dacc.gt.amax) amax=dacc
endif
enddo
enddo
endif
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
do j=1,3
c accel(j)=accel(j)+d_a(j,i+nres)-d_a_old(j,i+nres)
accel_old(j)=accel_old(j)+d_a_old(j,i+nres)
c if (dabs(accel(j)).gt.amax) amax=dabs(accel(j))
if (dabs(accel(j)).gt.dabs(accel_old(j))) then
dacc=dabs(accel(j)-accel_old(j))
+c write (iout,*) "side-chain",i,dacc
if (dacc.gt.amax) amax=dacc
endif
enddo
enddo
endif
c Side chains
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
do j=1,3
epdriftij=
& dabs((d_a(j,i+nres)-d_a_old(j,i+nres))*gxcart(j,i))
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
inres=i+nres
do j=1,3
d_t(j,inres)=fact*d_t(j,inres)
stdforcp(i)=stdfp*dsqrt(gamp)
enddo
do i=nnt,nct
- stdforcsc(i)=stdfsc(itype(i))*dsqrt(gamsc(itype(i)))
+ stdforcsc(i)=stdfsc(iabs(itype(i)))
+ & *dsqrt(gamsc(iabs(itype(i))))
enddo
endif
c Open the pdb file for snapshotshots
call chainbuild_cart
call kinetic(EK)
if (tbf) then
- call verlet_bath(EK)
+ call verlet_bath
endif
kinetic_T=2.0d0/(dimen3*Rb)*EK
if(me.eq.king.or..not.out1file)then
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
do j=1,3
ind=ind+1
d_t(j,i+nres)=d_t_work(ind)
ind=ind+3
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
do j=1,3
dc_work(ind+j)=dc_old(j,i+nres)
d_t_work(ind+j)=d_t_old(j,i+nres)
ind=ind+3
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
inres=i+nres
do j=1,3
d_t(j,inres)=d_t_work(ind+j)
ind=ind+3
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
do j=1,3
dc_work(ind+j)=dc_old(j,i+nres)
d_t_work(ind+j)=d_t_old(j,i+nres)
ind=ind+3
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
inres=i+nres
do j=1,3
dc(j,inres)=dc_work(ind+j)
ind=ind+3
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
inres=i+nres
do j=1,3
d_t(j,inres)=d_t_work(ind+j)
CPPFLAGS = -DLINUX -DUNRES -DMP -DMPI \
-DPGI -DSPLITELE -DISNAN -DAMD64 \
-DPROCOR -DLANG0 \
- -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
+ -DSCCORPDB
+# -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
+# -DSCCORPDB
## -DPROCOR
## -DMOMENT
#-DCO_BIAS
#FC= /usr/local/opt/intel/compiler60/ia32/bin/ifc
FC= ifort
-OPT = -O3 -ip -w
-
+#OPT = -O3 -ip -w
+OPT = -g -CB
+#OPT = -g
CFLAGS = -DSGI -c
FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include
FFLAGS2 = -c -w -O0 -I$(INSTALL_DIR)/include
FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report -I$(INSTALL_DIR)/include
-BIN = ../../../bin/unres/MD/unres_Tc_procor_oldparm_em64-D-symetr.exe
-#LIBS = -L$(INSTALL_DIR)/lib_pgi -lmpich ../../lib/xdrf/libxdrf.a
+BIN = ../../../bin/unres/MD-M/unres_Tc_procor_newparm_em64-D-symetr.exe
+#LIBS = -L$(INSTALL_DIR)/lib_pgi -lmpich xdrf/libxdrf.a
#LIBS = -L$(INSTALL_DIR)/lib_ifort -lmpich xdrf/libxdrf.a
-LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdrf.a -g -d2 -CA -CB
+LIBS = -L$(INSTALL_DIR)/lib -lmpich ../../lib/xdrf_em64/libxdrf.a -g -d2 -CA -CB
ARCH = LINUX
PP = /lib/cpp -P
cc -o compinfo compinfo.c
./compinfo | true
${FC} ${FFLAGS} cinfo.f
- ${FC} ${OPT} -Wl,-M ${object} proc_proc.o cinfo.o ${LIBS} -o ${BIN}
+ ${FC} ${OPT} ${object} proc_proc.o cinfo.o ${LIBS} -o ${BIN}
+ #${FC} ${OPT} -Wl,-M ${object} proc_proc.o cinfo.o ${LIBS} -o ${BIN}
clean:
proc_proc.o: proc_proc.c
${CC} ${CFLAGS} proc_proc.c
+
+ add.o: add.f
+ ${FC} ${FFLAGS2} add.f
+
+ blas.o: blas.f
+ ${FC} ${FFLAGS2} blas.f
+
+ eigen.o: eigen.f
+ ${FC} ${FFLAGS2} eigen.f
energia(17)=estr
energia(20)=Uconst+Uconst_back
energia(21)=esccor
+c Here are the energies showed per procesor if the are more processors
+c per molecule then we sum it up in sum_energy subroutine
c print *," Processor",myrank," calls SUM_ENERGY"
call sum_energy(energia,.true.)
c print *," Processor",myrank," left SUM_ENERGY"
#ifdef SPLITELE
etot=wsc*evdw+wscp*evdw2+welec*ees+wvdwpp*evdw1
& +wang*ebe+wtor*etors+wscloc*escloc
- & +wstrain*ehpb+nss*ebr+wcorr*ecorr+wcorr5*ecorr5
+ & +wstrain*ehpb+wcorr*ecorr+wcorr5*ecorr5
& +wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3
& +wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d
& +wbond*estr+Uconst+wsccor*esccor
#else
etot=wsc*evdw+wscp*evdw2+welec*(ees+evdw1)
& +wang*ebe+wtor*etors+wscloc*escloc
- & +wstrain*ehpb+nss*ebr+wcorr*ecorr+wcorr5*ecorr5
+ & +wstrain*ehpb+wcorr*ecorr+wcorr5*ecorr5
& +wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3
& +wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d
& +wbond*estr+Uconst+wsccor*esccor
#ifdef MPI
include 'mpif.h'
double precision gradbufc(3,maxres),gradbufx(3,maxres),
- & glocbuf(4*maxres),gradbufc_sum(3,maxres)
+ & glocbuf(4*maxres),gradbufc_sum(3,maxres),gloc_scbuf(3,maxres)
#endif
include 'COMMON.SETUP'
include 'COMMON.IOUNITS'
include 'COMMON.CONTROL'
include 'COMMON.TIME1'
include 'COMMON.MAXGRAD'
+ include 'COMMON.SCCOR'
#ifdef TIMING
time01=MPI_Wtime()
#endif
& +wturn3*gel_loc_turn3(i)
& +wturn6*gel_loc_turn6(i)
& +wel_loc*gel_loc_loc(i)
- & +wsccor*gsccor_loc(i)
enddo
#ifdef DEBUG
write (iout,*) "gloc after adding corr"
do i=1,4*nres
glocbuf(i)=gloc(i,icg)
enddo
+#define DEBUG
+#ifdef DEBUG
+ write (iout,*) "gloc_sc before reduce"
+ do i=1,nres
+ do j=1,1
+ write (iout,*) i,j,gloc_sc(j,i,icg)
+ enddo
+ enddo
+#endif
+#undef DEBUG
+ do i=1,nres
+ do j=1,3
+ gloc_scbuf(j,i)=gloc_sc(j,i,icg)
+ enddo
+ enddo
time00=MPI_Wtime()
call MPI_Barrier(FG_COMM,IERR)
time_barrier_g=time_barrier_g+MPI_Wtime()-time00
call MPI_Reduce(glocbuf(1),gloc(1,icg),4*nres,
& MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR)
time_reduce=time_reduce+MPI_Wtime()-time00
+ call MPI_Reduce(gloc_scbuf(1,1),gloc_sc(1,1,icg),3*nres,
+ & MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR)
+ time_reduce=time_reduce+MPI_Wtime()-time00
+#define DEBUG
+#ifdef DEBUG
+ write (iout,*) "gloc_sc after reduce"
+ do i=1,nres
+ do j=1,1
+ write (iout,*) i,j,gloc_sc(j,i,icg)
+ enddo
+ enddo
+#endif
+#undef DEBUG
#ifdef DEBUG
write (iout,*) "gloc after reduce"
do i=1,4*nres
c write(iout,*)'Entering ELJ nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
cd write (iout,*) 'i=',i,' iint=',iint,' istart=',istart(i,iint),
cd & 'iend=',iend(i,iint)
do j=istart(i,iint),iend(i,iint)
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
zj=c(3,nres+j)-zi
c print *,'Entering ELJK nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
C
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
zj=c(3,nres+j)-zi
c endif
ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
ind=ind+1
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
c dscj_inv=dsc_inv(itypj)
dscj_inv=vbld_inv(j+nres)
chi1=chi(itypi,itypj)
c if (icall.eq.0) lprn=.false.
ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
ind=ind+1
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
c dscj_inv=dsc_inv(itypj)
dscj_inv=vbld_inv(j+nres)
c write (iout,*) "j",j,dsc_inv(itypj),dscj_inv,
c if (icall.eq.0) lprn=.true.
ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
ind=ind+1
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
c dscj_inv=dsc_inv(itypj)
dscj_inv=vbld_inv(j+nres)
sig0ij=sigma(itypi,itypj)
cd print *,'Entering Esoft_sphere nnt=',nnt,' nct=',nct
evdw=0.0D0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
cd write (iout,*) 'i=',i,' iint=',iint,' istart=',istart(i,iint),
cd & 'iend=',iend(i,iint)
do j=istart(i,iint),iend(i,iint)
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
zj=c(3,nres+j)-zi
eello_turn4=0.0d0
ind=0
do i=iatel_s,iatel_e
- if (itype(i).eq.21 .or. itype(i+1).eq.21) cycle
+ if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
dxi=dc(1,i)
dyi=dc(2,i)
dzi=dc(3,i)
num_conti=0
c write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
do j=ielstart(i),ielend(i)
- if (itype(j).eq.21 .or. itype(j+1).eq.21) cycle
+ if (itype(j).eq.ntyp1 .or. itype(j+1).eq.ntyp1) cycle
ind=ind+1
iteli=itel(i)
itelj=itel(j)
enddo
c if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then
if (i.gt. nnt+1 .and. i.lt.nct+1) then
- iti1 = itortyp(itype(i-1))
+ if (itype(i-1).le.ntyp) then
+ iti1 = itortyp(itype(i-1))
+ else
+ iti1=ntortyp+1
+ endif
else
iti1=ntortyp+1
endif
C Loop over i,i+2 and i,i+3 pairs of the peptide groups
C
do i=iturn3_start,iturn3_end
- if (itype(i).eq.21 .or. itype(i+1).eq.21
- & .or. itype(i+2).eq.21 .or. itype(i+3).eq.21) cycle
+ if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1
+ & .or. itype(i+2).eq.ntyp1 .or. itype(i+3).eq.ntyp1) cycle
dxi=dc(1,i)
dyi=dc(2,i)
dzi=dc(3,i)
num_cont_hb(i)=num_conti
enddo
do i=iturn4_start,iturn4_end
- if (itype(i).eq.21 .or. itype(i+1).eq.21
- & .or. itype(i+3).eq.21
- & .or. itype(i+4).eq.21) cycle
+ if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1
+ & .or. itype(i+3).eq.ntyp1
+ & .or. itype(i+4).eq.ntyp1) cycle
dxi=dc(1,i)
dyi=dc(2,i)
dzi=dc(3,i)
zmedi=c(3,i)+0.5d0*dzi
num_conti=num_cont_hb(i)
call eelecij(i,i+3,ees,evdw1,eel_loc)
- if (wturn4.gt.0.0d0 .and. itype(i+2).ne.21)
+ if (wturn4.gt.0.0d0 .and. itype(i+2).ne.ntyp1)
& call eturn4(i,eello_turn4)
num_cont_hb(i)=num_conti
enddo ! i
c Loop over all pairs of interacting peptide groups except i,i+2 and i,i+3
c
do i=iatel_s,iatel_e
- if (itype(i).eq.21 .or. itype(i+1).eq.21) cycle
+ if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
dxi=dc(1,i)
dyi=dc(2,i)
dzi=dc(3,i)
num_conti=num_cont_hb(i)
do j=ielstart(i),ielend(i)
c write (iout,*) i,j,itype(i),itype(j)
- if (itype(j).eq.21 .or. itype(j+1).eq.21) cycle
+ if (itype(j).eq.ntyp1.or. itype(j+1).eq.ntyp1) cycle
call eelecij(i,j,ees,evdw1,eel_loc)
enddo ! j
num_cont_hb(i)=num_conti
cd & xmedi,ymedi,zmedi,xj,yj,zj
if (energy_dec) then
- write (iout,'(a6,2i5,0pf7.3)') 'evdw1',i,j,evdwij
+ write (iout,'(a6,2i5,0pf7.3,2i5,2e11.3)')
+ &'evdw1',i,j,evdwij
+ &,iteli,itelj,aaa,evdw1
write (iout,'(a6,2i5,0pf7.3)') 'ees',i,j,eesij
endif
if (energy_dec) write (iout,'(a6,2i5,0pf7.3)')
& 'eelloc',i,j,eel_loc_ij
+c write (iout,*) a22,muij(1),a23,muij(2),a32,muij(3)
eel_loc=eel_loc+eel_loc_ij
C Partial derivatives in virtual-bond dihedral angles gamma
cd print '(a)','Enter ESCP'
cd write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',iatscp_e
do i=iatscp_s,iatscp_e
- if (itype(i).eq.21 .or. itype(i+1).eq.21) cycle
+ if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
iteli=itel(i)
xi=0.5D0*(c(1,i)+c(1,i+1))
yi=0.5D0*(c(2,i)+c(2,i+1))
do iint=1,nscp_gr(i)
do j=iscpstart(i,iint),iscpend(i,iint)
- if (itype(j).eq.21) cycle
- itypj=itype(j)
+ if (itype(j).eq.ntyp1) cycle
+ itypj=iabs(itype(j))
C Uncomment following three lines for SC-p interactions
c xj=c(1,nres+j)-xi
c yj=c(2,nres+j)-yi
cd print '(a)','Enter ESCP'
cd write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',iatscp_e
do i=iatscp_s,iatscp_e
- if (itype(i).eq.21 .or. itype(i+1).eq.21) cycle
+ if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
iteli=itel(i)
xi=0.5D0*(c(1,i)+c(1,i+1))
yi=0.5D0*(c(2,i)+c(2,i+1))
do iint=1,nscp_gr(i)
do j=iscpstart(i,iint),iscpend(i,iint)
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
C Uncomment following three lines for SC-p interactions
c xj=c(1,nres+j)-xi
c yj=c(2,nres+j)-yi
endif
evdwij=e1+e2
evdw2=evdw2+evdwij
- if (energy_dec) write (iout,'(a6,2i5,0pf7.3)')
- & 'evdw2',i,j,evdwij
+ if (energy_dec) write (iout,'(a6,2i5,0pf7.3,2i3,3e11.3)')
+ & 'evdw2',i,j,evdwij,iteli,itypj,fac,aad(itypj,iteli),
+ & bad(itypj,iteli)
C
C Calculate contributions to the gradient in the virtual-bond and SC vectors.
C
cd write (iout,*) "i",i," ii",ii," iii",iii," jj",jj," jjj",jjj
C 24/11/03 AL: SS bridges handled separately because of introducing a specific
C distance and angle dependent SS bond potential.
- if (ii.gt.nres .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then
+ if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and.
+ & iabs(itype(jjj)).eq.1) then
call ssbond_ene(iii,jjj,eij)
ehpb=ehpb+2*eij
cd write (iout,*) "eij",eij
include 'COMMON.VAR'
include 'COMMON.IOUNITS'
double precision erij(3),dcosom1(3),dcosom2(3),gg(3)
- itypi=itype(i)
+ itypi=iabs(itype(i))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
dzi=dc_norm(3,nres+i)
c dsci_inv=dsc_inv(itypi)
dsci_inv=vbld_inv(nres+i)
- itypj=itype(j)
+ itypj=iabs(itype(j))
c dscj_inv=dsc_inv(itypj)
dscj_inv=vbld_inv(nres+j)
xj=c(1,nres+j)-xi
cosphi=om12-om1*om2
eij=akcm*deltad*deltad+akth*(deltat1*deltat1+deltat2*deltat2)
& +akct*deltad*deltat12
- & +v1ss*cosphi+v2ss*cosphi*cosphi+v3ss*cosphi*cosphi*cosphi
+ & +v1ss*cosphi+v2ss*cosphi*cosphi+v3ss*cosphi*cosphi*cosphi+ebr
c write(iout,*) i,j,"rij",rij,"d0cm",d0cm," akcm",akcm," akth",akth,
c & " akct",akct," deltad",deltad," deltat",deltat1,deltat2,
c & " deltat12",deltat12," eij",eij
estr=0.0d0
estr1=0.0d0
do i=ibondp_start,ibondp_end
- if (itype(i-1).eq.21 .or. itype(i).eq.21) then
+ if (itype(i-1).eq.ntyp1 .or. itype(i).eq.ntyp1) then
estr1=estr1+gnmr1(vbld(i),-1.0d0,distchainmax)
do j=1,3
gradb(j,i-1)=gnmr1prim(vbld(i),-1.0d0,distchainmax)
c 09/18/07 AL: multimodal bond potential based on AM1 CA-SC PMF's included
c
do i=ibond_start,ibond_end
- iti=itype(i)
- if (iti.ne.10 .and. iti.ne.21) then
+ iti=iabs(itype(i))
+ if (iti.ne.10 .and. iti.ne.ntyp1) then
nbi=nbondterm(iti)
if (nbi.eq.1) then
diff=vbld(i+nres)-vbldsc0(1,iti)
etheta=0.0D0
c write (*,'(a,i2)') 'EBEND ICG=',icg
do i=ithet_start,ithet_end
- if (itype(i-1).eq.21) cycle
+ if (itype(i-1).eq.ntyp1) cycle
C Zero the energy function and its derivative at 0 or pi.
call splinthet(theta(i),0.5d0*delta,ss,ssd)
it=itype(i-1)
- if (i.gt.3 .and. itype(i-2).ne.21) then
+ ichir1=isign(1,itype(i-2))
+ ichir2=isign(1,itype(i))
+ if (itype(i-2).eq.10) ichir1=isign(1,itype(i-1))
+ if (itype(i).eq.10) ichir2=isign(1,itype(i-1))
+ if (itype(i-1).eq.10) then
+ itype1=isign(10,itype(i-2))
+ ichir11=isign(1,itype(i-2))
+ ichir12=isign(1,itype(i-2))
+ itype2=isign(10,itype(i))
+ ichir21=isign(1,itype(i))
+ ichir22=isign(1,itype(i))
+ endif
+
+ if (i.gt.3 .and. itype(i-2).ne.ntyp1) then
#ifdef OSF
phii=phi(i)
if (phii.ne.phii) phii=150.0
y(1)=0.0D0
y(2)=0.0D0
endif
- if (i.lt.nres .and. itype(i).ne.21) then
+ if (i.lt.nres .and. itype(i).ne.ntyp1) then
#ifdef OSF
phii1=phi(i+1)
if (phii1.ne.phii1) phii1=150.0
C In following comments this theta will be referred to as t_c.
thet_pred_mean=0.0d0
do k=1,2
- athetk=athet(k,it)
- bthetk=bthet(k,it)
- thet_pred_mean=thet_pred_mean+athetk*y(k)+bthetk*z(k)
+ athetk=athet(k,it,ichir1,ichir2)
+ bthetk=bthet(k,it,ichir1,ichir2)
+ if (it.eq.10) then
+ athetk=athet(k,itype1,ichir11,ichir12)
+ bthetk=bthet(k,itype2,ichir21,ichir22)
+ endif
+ thet_pred_mean=thet_pred_mean+athetk*y(k)+bthetk*z(k)
enddo
dthett=thet_pred_mean*ssd
thet_pred_mean=thet_pred_mean*ss+a0thet(it)
C Derivatives of the "mean" values in gamma1 and gamma2.
- dthetg1=(-athet(1,it)*y(2)+athet(2,it)*y(1))*ss
- dthetg2=(-bthet(1,it)*z(2)+bthet(2,it)*z(1))*ss
+ dthetg1=(-athet(1,it,ichir1,ichir2)*y(2)
+ &+athet(2,it,ichir1,ichir2)*y(1))*ss
+ dthetg2=(-bthet(1,it,ichir1,ichir2)*z(2)
+ & +bthet(2,it,ichir1,ichir2)*z(1))*ss
+ if (it.eq.10) then
+ dthetg1=(-athet(1,itype1,ichir11,ichir12)*y(2)
+ &+athet(2,itype1,ichir11,ichir12)*y(1))*ss
+ dthetg2=(-bthet(1,itype2,ichir21,ichir22)*z(2)
+ & +bthet(2,itype2,ichir21,ichir22)*z(1))*ss
+ endif
if (theta(i).gt.pi-delta) then
call theteng(pi-delta,thet_pred_mean,theta0(it),f0,fprim0,
& E_tc0)
logical lprn /.false./, lprn1 /.false./
etheta=0.0D0
do i=ithet_start,ithet_end
- if (itype(i-1).eq.21) cycle
+ if (itype(i-1).eq.ntyp1) cycle
+ if (iabs(itype(i+1)).eq.20) iblock=2
+ if (iabs(itype(i+1)).ne.20) iblock=1
dethetai=0.0d0
dephii=0.0d0
dephii1=0.0d0
theti2=0.5d0*theta(i)
- ityp2=ithetyp(itype(i-1))
+ ityp2=ithetyp((itype(i-1)))
do k=1,nntheterm
coskt(k)=dcos(k*theti2)
sinkt(k)=dsin(k*theti2)
enddo
- if (i.gt.3 .and. itype(i-2).ne.21) then
+ if (i.gt.3 .and. itype(i-2).ne.ntyp1) then
#ifdef OSF
phii=phi(i)
if (phii.ne.phii) phii=150.0
#else
phii=phi(i)
#endif
- ityp1=ithetyp(itype(i-2))
+ ityp1=ithetyp((itype(i-2)))
+C propagation of chirality for glycine type
do k=1,nsingle
cosph1(k)=dcos(k*phii)
sinph1(k)=dsin(k*phii)
sinph1(k)=0.0d0
enddo
endif
- if (i.lt.nres .and. itype(i).ne.21) then
+ if (i.lt.nres .and. itype(i).ne.ntyp1) then
#ifdef OSF
phii1=phi(i+1)
if (phii1.ne.phii1) phii1=150.0
#else
phii1=phi(i+1)
#endif
- ityp3=ithetyp(itype(i))
+ ityp3=ithetyp((itype(i)))
do k=1,nsingle
cosph2(k)=dcos(k*phii1)
sinph2(k)=dsin(k*phii1)
sinph2(k)=0.0d0
enddo
endif
- ethetai=aa0thet(ityp1,ityp2,ityp3)
+ ethetai=aa0thet(ityp1,ityp2,ityp3,iblock)
do k=1,ndouble
do l=1,k-1
ccl=cosph1(l)*cosph2(k-l)
enddo
endif
do k=1,ntheterm
- ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3)*sinkt(k)
- dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3)
+ ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3,iblock)*sinkt(k)
+ dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3,iblock)
& *coskt(k)
if (lprn)
- & write (iout,*) "k",k," aathet",aathet(k,ityp1,ityp2,ityp3),
+ & write (iout,*) "k",k,"
+ & aathet",aathet(k,ityp1,ityp2,ityp3,iblock),
& " ethetai",ethetai
enddo
if (lprn) then
endif
do m=1,ntheterm2
do k=1,nsingle
- aux=bbthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)
- & +ccthet(k,m,ityp1,ityp2,ityp3)*sinph1(k)
- & +ddthet(k,m,ityp1,ityp2,ityp3)*cosph2(k)
- & +eethet(k,m,ityp1,ityp2,ityp3)*sinph2(k)
+ aux=bbthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k)
+ & +ccthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k)
+ & +ddthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k)
+ & +eethet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k)
ethetai=ethetai+sinkt(m)*aux
dethetai=dethetai+0.5d0*m*aux*coskt(m)
dephii=dephii+k*sinkt(m)*(
- & ccthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)-
- & bbthet(k,m,ityp1,ityp2,ityp3)*sinph1(k))
+ & ccthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k)-
+ & bbthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k))
dephii1=dephii1+k*sinkt(m)*(
- & eethet(k,m,ityp1,ityp2,ityp3)*cosph2(k)-
- & ddthet(k,m,ityp1,ityp2,ityp3)*sinph2(k))
+ & eethet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k)-
+ & ddthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k))
if (lprn)
& write (iout,*) "m",m," k",k," bbthet",
- & bbthet(k,m,ityp1,ityp2,ityp3)," ccthet",
- & ccthet(k,m,ityp1,ityp2,ityp3)," ddthet",
- & ddthet(k,m,ityp1,ityp2,ityp3)," eethet",
- & eethet(k,m,ityp1,ityp2,ityp3)," ethetai",ethetai
+ & bbthet(k,m,ityp1,ityp2,ityp3,iblock)," ccthet",
+ & ccthet(k,m,ityp1,ityp2,ityp3,iblock)," ddthet",
+ & ddthet(k,m,ityp1,ityp2,ityp3,iblock)," eethet",
+ & eethet(k,m,ityp1,ityp2,ityp3,iblock)," ethetai",ethetai
enddo
enddo
if (lprn)
do m=1,ntheterm3
do k=2,ndouble
do l=1,k-1
- aux=ffthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)
+ aux=ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)
ethetai=ethetai+sinkt(m)*aux
dethetai=dethetai+0.5d0*m*coskt(m)*aux
dephii=dephii+l*sinkt(m)*(
- & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)-
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+ & -ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)-
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l))
dephii1=dephii1+(k-l)*sinkt(m)*(
- & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)-
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+ & -ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)-
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l))
if (lprn) then
write (iout,*) "m",m," k",k," l",l," ffthet",
- & ffthet(l,k,m,ityp1,ityp2,ityp3),
- & ffthet(k,l,m,ityp1,ityp2,ityp3)," ggthet",
- & ggthet(l,k,m,ityp1,ityp2,ityp3),
- & ggthet(k,l,m,ityp1,ityp2,ityp3)," ethetai",ethetai
+ & ffthet(l,k,m,ityp1,ityp2,ityp3,iblock),
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)," ggthet",
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock),
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock),
+ & " ethetai",ethetai
write (iout,*) cosph1ph2(l,k)*sinkt(m),
& cosph1ph2(k,l)*sinkt(m),
& sinph1ph2(l,k)*sinkt(m),sinph1ph2(k,l)*sinkt(m)
enddo
enddo
10 continue
- if (lprn1) write (iout,'(i2,3f8.1,9h ethetai ,f10.5)')
+c lprn1=.true.
+ if (lprn1)
+ & write (iout,'(i2,3f8.1,9h ethetai ,f10.5)')
& i,theta(i)*rad2deg,phii*rad2deg,
& phii1*rad2deg,ethetai
+c lprn1=.false.
etheta=etheta+ethetai
if (i.gt.3) gloc(i-3,icg)=gloc(i-3,icg)+wang*dephii
if (i.lt.nres) gloc(i-2,icg)=gloc(i-2,icg)+wang*dephii1
c write (iout,'(a)') 'ESC'
do i=loc_start,loc_end
it=itype(i)
- if (it.eq.21) cycle
+ if (it.eq.ntyp1) cycle
if (it.eq.10) goto 1
- nlobit=nlob(it)
+ nlobit=nlob(iabs(it))
c print *,'i=',i,' it=',it,' nlobit=',nlobit
c write (iout,*) 'i=',i,' ssa=',ssa,' ssad=',ssad
theti=theta(i+1)-pipol
do j=1,nlobit
#ifdef OSF
- adexp=bsc(j,it)-0.5D0*contr(j,iii)+emin
+ adexp=bsc(j,iabs(it))-0.5D0*contr(j,iii)+emin
if(adexp.ne.adexp) adexp=1.0
expfac=dexp(adexp)
#else
- expfac=dexp(bsc(j,it)-0.5D0*contr(j,iii)+emin)
+ expfac=dexp(bsc(j,iabs(it))-0.5D0*contr(j,iii)+emin)
#endif
cd print *,'j=',j,' expfac=',expfac
escloc_i=escloc_i+expfac
dersc12=0.0d0
do j=1,nlobit
- expfac=dexp(bsc(j,it)-0.5D0*contr(j)+emin)
+ expfac=dexp(bsc(j,iabs(it))-0.5D0*contr(j)+emin)
escloc_i=escloc_i+expfac
do k=1,2
dersc(k)=dersc(k)+Ax(k,j)*expfac
delta=0.02d0*pi
escloc=0.0D0
do i=loc_start,loc_end
- if (itype(i).eq.21) cycle
+ if (itype(i).eq.ntyp1) cycle
costtab(i+1) =dcos(theta(i+1))
sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
cosfac=dsqrt(cosfac2)
sinfac2=0.5d0/(1.0d0-costtab(i+1))
sinfac=dsqrt(sinfac2)
- it=itype(i)
+ it=iabs(itype(i))
if (it.eq.10) goto 1
c
C Compute the axes of tghe local cartesian coordinates system; store in
y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
enddo
do j = 1,3
- z_prime(j) = -uz(j,i-1)
+ z_prime(j) = -uz(j,i-1)*dsign(1.0d0,dfloat(itype(i)))
enddo
c write (2,*) "i",i
c write (2,*) "x_prime",(x_prime(j),j=1,3)
C Compute the energy of the ith side cbain
C
c write (2,*) "xx",xx," yy",yy," zz",zz
- it=itype(i)
+ it=iabs(itype(i))
do j = 1,65
x(j) = sc_parmin(j,it)
enddo
Cc diagnostics - remove later
xx1 = dcos(alph(2))
yy1 = dsin(alph(2))*dcos(omeg(2))
- zz1 = -dsin(alph(2))*dsin(omeg(2))
+ zz1 = -dsign(1.0,dfloat(itype(i)))*dsin(alph(2))*dsin(omeg(2))
write(2,'(3f8.1,3f9.3,1x,3f9.3)')
& alph(2)*rad2deg,omeg(2)*rad2deg,theta(3)*rad2deg,xx,yy,zz,
& xx1,yy1,zz1
c & dscp1,dscp2,sumene
c sumene = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
escloc = escloc + sumene
-c write (2,*) "i",i," escloc",sumene,escloc
+c write (2,*) "i",i," escloc",sumene,escloc,it,itype(i)
+c & ,zz,xx,yy
+c#define DEBUG
#ifdef DEBUG
C
C This section to check the numerical derivatives of the energy of ith side
C
C Compute the gradient of esc
C
+c zz=zz*dsign(1.0,dfloat(itype(i)))
pom_s1=(1.0d0+x(63))/(0.1d0 + dscp1)**2
pom_s16=6*(1.0d0+x(64))/(0.1d0 + dscp1**6)**2
pom_s2=(1.0d0+x(65))/(0.1d0 + dscp2)**2
& +(sumene2x+sumene4x*cost2tab(i+1))*(s2+s2_6)
& +(pom1+pom2)*pom_dx
#ifdef DEBUG
- write(2,*), "de_dxx = ", de_dxx,de_dxx_num
+ write(2,*), "de_dxx = ", de_dxx,de_dxx_num,itype(i)
#endif
C
sumene1y=x(3) + 2*x(6)*yy + x(9)*xx + x(10)*zz
& +(sumene2y+sumene4y*cost2tab(i+1))*(s2+s2_6)
& +(pom1-pom2)*pom_dy
#ifdef DEBUG
- write(2,*), "de_dyy = ", de_dyy,de_dyy_num
+ write(2,*), "de_dyy = ", de_dyy,de_dyy_num,itype(i)
#endif
C
de_dzz =(x(24) +2*x(27)*zz +x(28)*xx +x(30)*yy
& +x(60)*xx*yy)*cost2tab(i+1)*(s2+s2_6)
& + ( x(14) + 2*x(17)*zz+ x(18)*xx + x(20)*yy)*(s2+s2_6)
#ifdef DEBUG
- write(2,*), "de_dzz = ", de_dzz,de_dzz_num
+ write(2,*), "de_dzz = ", de_dzz,de_dzz_num,itype(i)
#endif
C
de_dt = 0.5d0*sumene3*cost2tab(i+1)*(s1+s1_6)
& -0.5d0*sumene4*sint2tab(i+1)*(s2+s2_6)
& +pom1*pom_dt1+pom2*pom_dt2
#ifdef DEBUG
- write(2,*), "de_dt = ", de_dt,de_dt_num
+ write(2,*), "de_dt = ", de_dt,de_dt_num,itype(i)
#endif
+c#undef DEBUG
c
C
cossc=scalar(dc_norm(1,i),dc_norm(1,i+nres))
dZZ_Ci1(k)=0.0d0
dZZ_Ci(k)=0.0d0
do j=1,3
- dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)*dC_norm(j,i+nres)
- dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)*dC_norm(j,i+nres)
+ dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)
+ & *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres)
+ dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)
+ & *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres)
enddo
dXX_XYZ(k)=vbld_inv(i+nres)*(x_prime(k)-xx*dC_norm(k,i+nres))
dYY_XYZ(k)=vbld_inv(i+nres)*(y_prime(k)-yy*dC_norm(k,i+nres))
- dZZ_XYZ(k)=vbld_inv(i+nres)*(z_prime(k)-zz*dC_norm(k,i+nres))
+ dZZ_XYZ(k)=vbld_inv(i+nres)*
+ & (z_prime(k)-zz*dC_norm(k,i+nres))
c
dt_dCi(k) = -dt_dCi(k)/sinttab(i+1)
dt_dCi1(k)= -dt_dCi1(k)/sinttab(i+1)
etors=0.0D0
do i=iphi_start,iphi_end
etors_ii=0.0D0
- if (itype(i-2).eq.21 .or. itype(i-1).eq.21
- & .or. itype(i).eq.21) cycle
+ if (itype(i-2).eq.ntyp1.or. itype(i-1).eq.ntyp1
+ & .or. itype(i).eq.ntyp1) cycle
itori=itortyp(itype(i-2))
itori1=itortyp(itype(i-1))
phii=phi(i)
c lprn=.true.
etors=0.0D0
do i=iphi_start,iphi_end
- if (itype(i-2).eq.21 .or. itype(i-1).eq.21
- & .or. itype(i).eq.21) cycle
+ if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1
+ & .or. itype(i).eq.ntyp1) cycle
etors_ii=0.0D0
+ if (iabs(itype(i)).eq.20) then
+ iblock=2
+ else
+ iblock=1
+ endif
itori=itortyp(itype(i-2))
itori1=itortyp(itype(i-1))
phii=phi(i)
gloci=0.0D0
C Regular cosine and sine terms
- do j=1,nterm(itori,itori1)
- v1ij=v1(j,itori,itori1)
- v2ij=v2(j,itori,itori1)
+ do j=1,nterm(itori,itori1,iblock)
+ v1ij=v1(j,itori,itori1,iblock)
+ v2ij=v2(j,itori,itori1,iblock)
cosphi=dcos(j*phii)
sinphi=dsin(j*phii)
etors=etors+v1ij*cosphi+v2ij*sinphi
C
cosphi=dcos(0.5d0*phii)
sinphi=dsin(0.5d0*phii)
- do j=1,nlor(itori,itori1)
+ do j=1,nlor(itori,itori1,iblock)
vl1ij=vlor1(j,itori,itori1)
vl2ij=vlor2(j,itori,itori1)
vl3ij=vlor3(j,itori,itori1)
gloci=gloci+vl1ij*(vl3ij*cosphi-vl2ij*sinphi)*pom
enddo
C Subtract the constant term
- etors=etors-v0(itori,itori1)
+ etors=etors-v0(itori,itori1,iblock)
if (energy_dec) write (iout,'(a6,i5,0pf7.3)')
- & 'etor',i,etors_ii-v0(itori,itori1)
+ & 'etor',i,etors_ii-v0(itori,itori1,iblock)
if (lprn)
& write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)')
& restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
- & (v1(j,itori,itori1),j=1,6),(v2(j,itori,itori1),j=1,6)
+ & (v1(j,itori,itori1,iblock),j=1,6),
+ & (v2(j,itori,itori1,iblock),j=1,6)
gloc(i-3,icg)=gloc(i-3,icg)+wtor*gloci
c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg)
enddo
lprn=.false.
c lprn=.true.
etors_d=0.0D0
+c write(iout,*) "a tu??"
do i=iphid_start,iphid_end
- if (itype(i-2).eq.21 .or. itype(i-1).eq.21
- & .or. itype(i).eq.21 .or. itype(i+1).eq.21) cycle
+ if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1
+ & .or. itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
itori=itortyp(itype(i-2))
itori1=itortyp(itype(i-1))
itori2=itortyp(itype(i))
phii1=phi(i+1)
gloci1=0.0D0
gloci2=0.0D0
+ iblock=1
+ if (iabs(itype(i+1)).eq.20) iblock=2
+
C Regular cosine and sine terms
- do j=1,ntermd_1(itori,itori1,itori2)
- v1cij=v1c(1,j,itori,itori1,itori2)
- v1sij=v1s(1,j,itori,itori1,itori2)
- v2cij=v1c(2,j,itori,itori1,itori2)
- v2sij=v1s(2,j,itori,itori1,itori2)
+ do j=1,ntermd_1(itori,itori1,itori2,iblock)
+ v1cij=v1c(1,j,itori,itori1,itori2,iblock)
+ v1sij=v1s(1,j,itori,itori1,itori2,iblock)
+ v2cij=v1c(2,j,itori,itori1,itori2,iblock)
+ v2sij=v1s(2,j,itori,itori1,itori2,iblock)
cosphi1=dcos(j*phii)
sinphi1=dsin(j*phii)
cosphi2=dcos(j*phii1)
gloci1=gloci1+j*(v1sij*cosphi1-v1cij*sinphi1)
gloci2=gloci2+j*(v2sij*cosphi2-v2cij*sinphi2)
enddo
- do k=2,ntermd_2(itori,itori1,itori2)
+ do k=2,ntermd_2(itori,itori1,itori2,iblock)
do l=1,k-1
- v1cdij = v2c(k,l,itori,itori1,itori2)
- v2cdij = v2c(l,k,itori,itori1,itori2)
- v1sdij = v2s(k,l,itori,itori1,itori2)
- v2sdij = v2s(l,k,itori,itori1,itori2)
+ v1cdij = v2c(k,l,itori,itori1,itori2,iblock)
+ v2cdij = v2c(l,k,itori,itori1,itori2,iblock)
+ v1sdij = v2s(k,l,itori,itori1,itori2,iblock)
+ v2sdij = v2s(l,k,itori,itori1,itori2,iblock)
cosphi1p2=dcos(l*phii+(k-l)*phii1)
cosphi1m2=dcos(l*phii-(k-l)*phii1)
sinphi1p2=dsin(l*phii+(k-l)*phii1)
C Set lprn=.true. for debugging
lprn=.false.
c lprn=.true.
-c write (iout,*) "EBACK_SC_COR",iphi_start,iphi_end,nterm_sccor
+c write (iout,*) "EBACK_SC_COR",itau_start,itau_end
esccor=0.0D0
- do i=iphi_start,iphi_end
- if (itype(i-2).eq.21 .or. itype(i-1).eq.21) cycle
+ do i=itau_start,itau_end
+ if ((itype(i-2).eq.ntyp1).or.(itype(i-1).eq.ntyp1)) cycle
esccor_ii=0.0D0
- itori=itype(i-2)
- itori1=itype(i-1)
+ isccori=isccortyp(itype(i-2))
+ isccori1=isccortyp(itype(i-1))
+c write (iout,*) "EBACK_SC_COR",i,nterm_sccor(isccori,isccori1)
phii=phi(i)
+ do intertyp=1,3 !intertyp
+cc Added 09 May 2012 (Adasko)
+cc Intertyp means interaction type of backbone mainchain correlation:
+c 1 = SC...Ca...Ca...Ca
+c 2 = Ca...Ca...Ca...SC
+c 3 = SC...Ca...Ca...SCi
gloci=0.0D0
- do j=1,nterm_sccor
- v1ij=v1sccor(j,itori,itori1)
- v2ij=v2sccor(j,itori,itori1)
- cosphi=dcos(j*phii)
- sinphi=dsin(j*phii)
+ if (((intertyp.eq.3).and.((itype(i-2).eq.10).or.
+ & (itype(i-1).eq.10).or.(itype(i-2).eq.ntyp1).or.
+ & (itype(i-1).eq.ntyp1)))
+ & .or. ((intertyp.eq.1).and.((itype(i-2).eq.10)
+ & .or.(itype(i-2).eq.ntyp1).or.(itype(i-1).eq.ntyp1)
+ & .or.(itype(i).eq.ntyp1)))
+ & .or.((intertyp.eq.2).and.((itype(i-1).eq.10).or.
+ & (itype(i-1).eq.ntyp1).or.(itype(i-2).eq.ntyp1).or.
+ & (itype(i-3).eq.ntyp1)))) cycle
+ if ((intertyp.eq.2).and.(i.eq.4).and.(itype(1).eq.ntyp1)) cycle
+ if ((intertyp.eq.1).and.(i.eq.nres).and.(itype(nres).eq.ntyp1))
+ & cycle
+ do j=1,nterm_sccor(isccori,isccori1)
+ v1ij=v1sccor(j,intertyp,isccori,isccori1)
+ v2ij=v2sccor(j,intertyp,isccori,isccori1)
+ cosphi=dcos(j*tauangle(intertyp,i))
+ sinphi=dsin(j*tauangle(intertyp,i))
esccor=esccor+v1ij*cosphi+v2ij*sinphi
gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
enddo
+c write (iout,*) "EBACK_SC_COR",i,v1ij*cosphi+v2ij*sinphi,intertyp
+ gloc_sc(intertyp,i-3,icg)=gloc_sc(intertyp,i-3,icg)+wsccor*gloci
if (lprn)
& write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)')
- & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
- & (v1sccor(j,itori,itori1),j=1,6),(v2sccor(j,itori,itori1),j=1,6)
+ & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,isccori,isccori1,
+ & (v1sccor(j,intertyp,isccori,isccori1),j=1,6)
+ & ,(v2sccor(j,intertyp,isccori,isccori1),j=1,6)
gsccor_loc(i-3)=gsccor_loc(i-3)+gloci
+ enddo !intertyp
enddo
+
return
end
c----------------------------------------------------------------------------
igeom= 8
intin= 9
ithep= 11
+ ithep_pdb=51
irotam=12
+ irotam_pdb=52
itorp= 13
itordp= 23
ielep= 14
rr0(i)=0.0D0
a0thet(i)=0.0D0
do j=1,2
- athet(j,i)=0.0D0
- bthet(j,i)=0.0D0
+ do ichir1=-1,1
+ do ichir2=-1,1
+ athet(j,i,ichir1,ichir2)=0.0D0
+ bthet(j,i,ichir1,ichir2)=0.0D0
+ enddo
+ enddo
enddo
- do j=0,3
+ do j=0,3
polthet(j,i)=0.0D0
enddo
do j=1,3
enddo
nlob(ntyp1)=0
dsc(ntyp1)=0.0D0
- do i=1,maxtor
- itortyp(i)=0
- do j=1,maxtor
- do k=1,maxterm
- v1(k,j,i)=0.0D0
- v2(k,j,i)=0.0D0
+ do i=-maxtor,maxtor
+ itortyp(i)=0
+cc write (iout,*) "TU DOCHODZE",i,itortyp(i)
+ do iblock=1,2
+ do j=-maxtor,maxtor
+ do k=1,maxterm
+ v1(k,j,i,iblock)=0.0D0
+ v2(k,j,i,iblock)=0.0D0
enddo
enddo
+ enddo
enddo
+ do iblock=1,2
+ do i=-maxtor,maxtor
+ do j=-maxtor,maxtor
+ do k=-maxtor,maxtor
+ do l=1,maxtermd_1
+ v1c(1,l,i,j,k,iblock)=0.0D0
+ v1s(1,l,i,j,k,iblock)=0.0D0
+ v1c(2,l,i,j,k,iblock)=0.0D0
+ v1s(2,l,i,j,k,iblock)=0.0D0
+ enddo !l
+ do l=1,maxtermd_2
+ do m=1,maxtermd_2
+ v2c(m,l,i,j,k,iblock)=0.0D0
+ v2s(m,l,i,j,k,iblock)=0.0D0
+ enddo !m
+ enddo !l
+ enddo !k
+ enddo !j
+ enddo !i
+ enddo !iblock
+
do i=1,maxres
itype(i)=0
itel(i)=0
include 'COMMON.NAMES'
include 'COMMON.FFIELD'
data restyp /
+ &'DD','DAU','DAI','DDB','DSM','DPR','DLY','DAR','DHI','DAS','DGL',
+ & 'DSG','DGN','DSN','DTH',
+ &'DYY','DAL','DTY','DTR','DVA','DLE','DIL','DPN','MED','DCY','ZER',
&'CYS','MET','PHE','ILE','LEU','VAL','TRP','TYR','ALA','GLY','THR',
- &'SER','GLN','ASN','GLU','ASP','HIS','ARG','LYS','PRO','D'/
+ &'SER','GLN','ASN','GLU','ASP','HIS','ARG','LYS','PRO','SME','DBZ',
+ &'AIB','ABU','D'/
data onelet /
+ &'z','z','z','z','z','p','k','r','h','d','e','n','q','s','t','g',
+ &'a','y','w','v','l','i','f','m','c','x',
&'C','M','F','I','L','V','W','Y','A','G','T',
- &'S','Q','N','E','D','H','R','K','P','X'/
+ &'S','Q','N','E','D','H','R','K','P','z','z','z','z','X'/
data potname /'LJ','LJK','BP','GB','GBV'/
data ename /
& "EVDW SC-SC","EVDW2 SC-p","EES p-p","ECORR4 ","ECORR5 ",
include 'COMMON.IOUNITS'
include 'COMMON.DERIV'
include 'COMMON.CONTACTS'
- common /przechowalnia/ iturn3_start_all(0:MaxProcs),
- & iturn3_end_all(0:MaxProcs),iturn4_start_all(0:MaxProcs),
- & iturn4_end_all(0:MaxProcs),iatel_s_all(0:MaxProcs),
- & iatel_e_all(0:MaxProcs),ielstart_all(maxres,0:MaxProcs-1),
- & ielend_all(maxres,0:MaxProcs-1),
+ common /przechowalnia/ iturn3_start_all(0:max_fg_procs),
+ & iturn3_end_all(0:max_fg_procs),iturn4_start_all(0:max_fg_procs),
+ & iturn4_end_all(0:max_fg_procs),iatel_s_all(0:max_fg_procs),
+ &iatel_e_all(0:max_fg_procs),ielstart_all(maxres,0:max_fg_procs-1),
+ & ielend_all(maxres,0:max_fg_procs-1),
& ntask_cont_from_all(0:max_fg_procs-1),
& itask_cont_from_all(0:max_fg_procs-1,0:max_fg_procs-1),
& ntask_cont_to_all(0:max_fg_procs-1),
iphi_end=iturn3_end+2
iturn3_start=iturn3_start-1
iturn3_end=iturn3_end-1
+ call int_bounds(nres-3,itau_start,itau_end)
+ itau_start=itau_start+3
+ itau_end=itau_end+3
call int_bounds(nres-3,iphi1_start,iphi1_end)
iphi1_start=iphi1_start+3
iphi1_end=iphi1_end+3
idihconstr_end=ndih_constr
iphid_start=iphi_start
iphid_end=iphi_end-1
+ itau_start=4
+ itau_end=nres
ibond_start=2
ibond_end=nres-1
ibondp_start=nnt
include "COMMON.INTERACT"
include "COMMON.SETUP"
include "COMMON.IOUNITS"
- integer ii,jj,itask(4),ntask_cont_to,itask_cont_to(0:MaxProcs-1)
+ integer ii,jj,itask(4),ntask_cont_to,
+ &itask_cont_to(0:max_fg_procs-1)
logical flag
integer iturn3_start_all,iturn3_end_all,iturn4_start_all,
& iturn4_end_all,iatel_s_all,iatel_e_all,ielstart_all,ielend_all
- common /przechowalnia/ iturn3_start_all(0:MaxProcs),
- & iturn3_end_all(0:MaxProcs),iturn4_start_all(0:MaxProcs),
- & iturn4_end_all(0:MaxProcs),iatel_s_all(0:MaxProcs),
- & iatel_e_all(0:MaxProcs),ielstart_all(maxres,0:MaxProcs-1),
- & ielend_all(maxres,0:MaxProcs-1)
+ common /przechowalnia/ iturn3_start_all(0:max_fg_procs),
+ & iturn3_end_all(0:max_fg_procs),iturn4_start_all(0:max_fg_procs),
+ & iturn4_end_all(0:max_fg_procs),iatel_s_all(0:max_fg_procs),
+ &iatel_e_all(0:max_fg_procs),ielstart_all(maxres,0:max_fg_procs-1),
+ & ielend_all(maxres,0:max_fg_procs-1)
integer iproc,isent,k,l
c Determines whether to send interaction ii,jj to other processors; a given
c interaction can be sent to at most 2 processors.
include "COMMON.SETUP"
include "COMMON.IOUNITS"
integer ii,jj,itask(2),ntask_cont_from,
- & itask_cont_from(0:MaxProcs-1)
+ & itask_cont_from(0:max_fg_procs-1)
logical flag
integer iturn3_start_all,iturn3_end_all,iturn4_start_all,
& iturn4_end_all,iatel_s_all,iatel_e_all,ielstart_all,ielend_all
- common /przechowalnia/ iturn3_start_all(0:MaxProcs),
- & iturn3_end_all(0:MaxProcs),iturn4_start_all(0:MaxProcs),
- & iturn4_end_all(0:MaxProcs),iatel_s_all(0:MaxProcs),
- & iatel_e_all(0:MaxProcs),ielstart_all(maxres,0:MaxProcs-1),
- & ielend_all(maxres,0:MaxProcs-1)
+ common /przechowalnia/ iturn3_start_all(0:max_fg_procs),
+ & iturn3_end_all(0:max_fg_procs),iturn4_start_all(0:max_fg_procs),
+ & iturn4_end_all(0:max_fg_procs),iatel_s_all(0:max_fg_procs),
+ &iatel_e_all(0:max_fg_procs),ielstart_all(maxres,0:max_fg_procs-1),
+ & ielend_all(maxres,0:max_fg_procs-1)
integer iproc,k,l
do iproc=fg_rank+1,nfgtasks-1
do k=iturn3_start_all(iproc),iturn3_end_all(iproc)
subroutine add_task(iproc,ntask_cont,itask_cont)
implicit none
include "DIMENSIONS"
- integer iproc,ntask_cont,itask_cont(0:MaxProcs-1)
+ integer iproc,ntask_cont,itask_cont(0:max_fg_procs-1)
integer ii
do ii=1,ntask_cont
if (itask_cont(ii).eq.iproc) return
character*3 seq,atom,res
character*80 card
dimension sccor(3,20)
+ double precision e1(3),e2(3),e3(3)
integer rescode
+ logical fail
ibeg=1
lsecondary=.false.
nhfrag=0
else if (card(:3).eq.'TER') then
C End current chain
ires_old=ires+1
- itype(ires_old)=21
+ itype(ires_old)=ntyp1
ibeg=2
c write (iout,*) "Chain ended",ires,ishift,ires_old
if (unres_pdb) then
ishift=ires-1
if (res.ne.'GLY' .and. res.ne. 'ACE') then
ishift=ishift-1
- itype(1)=21
+ itype(1)=ntyp1
endif
c write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
ibeg=0
ires=ires-ishift
c write (2,*) "ires",ires," ishift",ishift
if (res.eq.'ACE') then
- ity=10
+ itype(ires)=10
else
itype(ires)=rescode(ires,res,0)
endif
nres=ires
do i=2,nres-1
c write (iout,*) i,itype(i)
- if (itype(i).eq.21) then
+ if (itype(i).eq.ntyp1) then
c write (iout,*) "dummy",i,itype(i)
do j=1,3
c(j,i)=((c(j,i-1)+c(j,i+1))/2+2*c(j,i-1)-c(j,i-2))/2
nstart_sup=1
if (itype(nres).ne.10) then
nres=nres+1
- itype(nres)=21
+ itype(nres)=ntyp1
if (unres_pdb) then
- c(1,nres)=c(1,nres-1)+3.8d0
- c(2,nres)=c(2,nres-1)
- c(3,nres)=c(3,nres-1)
+ C 2/15/2013 by Adam: corrected insertion of the last dummy residue
+ call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
+ if (fail) then
+ e2(1)=0.0d0
+ e2(2)=1.0d0
+ e2(3)=0.0d0
+ endif
+ do j=1,3
+ c(j,nres)=c(j,nres-1)-3.8d0*e2(j)
+ enddo
else
do j=1,3
dcj=c(j,nres-2)-c(j,nres-3)
c(j,nres+1)=c(j,1)
c(j,2*nres)=c(j,nres)
enddo
- if (itype(1).eq.21) then
+ if (itype(1).eq.ntyp1) then
nsup=nsup-1
nstart_sup=2
if (unres_pdb) then
- c(1,1)=c(1,2)-3.8d0
- c(2,1)=c(2,2)
- c(3,1)=c(3,2)
+ C 2/15/2013 by Adam: corrected insertion of the first dummy residue
+ call refsys(2,3,4,e1,e2,e3,fail)
+ if (fail) then
+ e2(1)=0.0d0
+ e2(2)=1.0d0
+ e2(3)=0.0d0
+ endif
+ do j=1,3
+ c(j,1)=c(j,2)-3.8d0*e2(j)
+ enddo
else
do j=1,3
dcj=c(j,4)-c(j,3)
lll=lll+1
cc write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
if (i.gt.1) then
- if ((itype(i-1).eq.21)) then
+ if ((itype(i-1).eq.ntyp1).and.(i.gt.2)) then
chain_length=lll-1
kkk=kkk+1
c write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
endif
enddo
enddo
+ write (iout,*) chain_length
+ if (chain_length.eq.0) chain_length=nres
do j=1,3
chain_rep(j,chain_length,symetr)=chain_rep(j,chain_length,1)
chain_rep(j,chain_length+nres,symetr)
#endif
do i=1,nres-1
iti=itype(i)
- if (iti.ne.21 .and. itype(i+1).ne.21 .and.
+ if (iti.ne.ntyp1 .and. itype(i+1).ne.ntyp1 .and.
& (dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0)) then
write (iout,'(a,i4)') 'Bad Cartesians for residue',i
ctest stop
enddo
enddo
do i=2,nres-1
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
do j=1,3
dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i))
enddo
sinfac2=0.5d0/(1.0d0-costtab(i+1))
sinfac=dsqrt(sinfac2)
it=itype(i)
- if (it.ne.10 .and. itype(i).ne.21) then
+ if (it.ne.10 .and. itype(i).ne.ntyp1) then
c
C Compute the axes of tghe local cartesian coordinates system; store in
c x_prime, y_prime and z_prime
do i=1,nres-1
vbld(i+1)=vbl
vbld_inv(i+1)=1.0d0/vbld(i+1)
- vbld(i+1+nres)=dsc(itype(i+1))
- vbld_inv(i+1+nres)=dsc_inv(itype(i+1))
+ vbld(i+1+nres)=dsc(iabs(itype(i+1)))
+ vbld_inv(i+1+nres)=dsc_inv(iabs(itype(i+1)))
c print *,vbld(i+1),vbld(i+1+nres)
enddo
return
ind=ind+3
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10) then
do j=1,3
d_t_work(ind+j)=d_t(j,i+nres)
enddo
ind=ind+3
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10) then
do j=1,3
friction(j,i+nres)=fric_work(ind+j)
enddo
enddo
x=0.0d0
+#ifdef MPI
time00=MPI_Wtime()
+#else
+ time00=tcpu()
+#endif
c Compute the stochastic forces acting on bodies. Store in force.
do i=nnt,nct-1
sig=stdforcp(i)
force(j,i+nres)=anorm_distr(x,sig2,lowb2,highb2)
enddo
enddo
+#ifdef MPI
time_fsample=time_fsample+MPI_Wtime()-time00
+#else
+ time_fsample=time_fsample+tcpu()-time00
+#endif
c Compute the stochastic forces acting on virtual-bond vectors.
do j=1,3
ff(j)=0.0d0
do j=1,3
ff(j)=ff(j)+force(j,i)
enddo
- if (itype(i+1).ne.21) then
+ if (itype(i+1).ne.ntyp1) then
do j=1,3
stochforc(j,i)=stochforc(j,i)+force(j,i+nres+1)
ff(j)=ff(j)+force(j,i+nres+1)
stochforc(j,0)=ff(j)+force(j,nnt+nres)
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10) then
do j=1,3
stochforc(j,i+nres)=force(j,i+nres)
enddo
ind=ind+3
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.21) then
+ if (itype(i).ne.10) then
do j=1,3
stochforcvec(ind+j)=stochforc(j,i+nres)
enddo
c------------------------------------------------------------------
subroutine setup_fricmat
implicit real*8 (a-h,o-z)
+#ifdef MPI
include 'mpif.h'
+#endif
include 'DIMENSIONS'
include 'COMMON.VAR'
include 'COMMON.CHAIN'
c Load the friction coefficients corresponding to side chains
m=nct-nnt
ind=0
+ gamsc(ntyp1)=1.0d0
do i=nnt,nct
ind=ind+1
ii = ind+m
iti=itype(i)
- gamvec(ii)=gamsc(iti)
+ gamvec(ii)=gamsc(iabs(iti))
enddo
if (surfarea) call sdarea(gamvec)
c if (lprn) then
if (nfgtasks.gt.1) then
if (fg_rank.eq.0) then
c The matching BROADCAST for fg processors is called in ERGASTULUM
+#ifdef MPI
time00=MPI_Wtime()
+#else
+ time00=tcpu()
+#endif
call MPI_Bcast(10,1,MPI_INTEGER,king,FG_COMM,IERROR)
+#ifdef MPI
time_Bcast=time_Bcast+MPI_Wtime()-time00
+#else
+ time_Bcast=time_Bcast+tcpu()-time00
+#endif
c print *,"Processor",myrank,
c & " BROADCAST iorder in SETUP_FRICMAT"
endif
c licznik=licznik+1
c write (iout,*) "setup_fricmat licznik",licznik
+#ifdef MPI
time00=MPI_Wtime()
+#else
+ time00=tcpu()
+#endif
c Scatter the friction matrix
call MPI_Scatterv(fricmat(1,1),nginv_counts(0),
& nginv_start(0),MPI_DOUBLE_PRECISION,fcopy(1,1),
& myginv_ng_count,MPI_DOUBLE_PRECISION,king,FG_COMM,IERROR)
- time_scatter=time_scatter+MPI_Wtime()-time00
#ifdef TIMING
+#ifdef MPI
+ time_scatter=time_scatter+MPI_Wtime()-time00
time_scatter_fmat=time_scatter_fmat+MPI_Wtime()-time00
+#else
+ time_scatter=time_scatter+tcpu()-time00
+ time_scatter_fmat=time_scatter_fmat+tcpu()-time00
+#endif
#endif
do i=1,dimen
do j=1,2*my_ng_count
include 'COMMON.INTERACT'
include 'COMMON.IOUNITS'
include 'COMMON.NAMES'
- double precision radius(maxres2),gamvec(maxres6)
+ double precision radius(maxres2),gamvec(maxres2)
parameter (twosix=1.122462048309372981d0)
- logical lprn /.true./
+ logical lprn /.false./
c
c determine new friction coefficients every few SD steps
c
timing.F
thread.F
unres.F
+ ssMD.F
)
if(Fortran_COMPILER_NAME STREQUAL "ifort")
set(UNRES_MD_SRC0 ${UNRES_MD_SRC0} prng.f )
+ elseif(Fortran_COMPILER_NAME STREQUAL "mpif90")
+ set(UNRES_MD_SRC0 ${UNRES_MD_SRC0} prng.f )
+ elseif(Fortran_COMPILER_NAME STREQUAL "f95")
+ set(UNRES_MD_SRC0 ${UNRES_MD_SRC0} prng.f )
+ elseif(Fortran_COMPILER_NAME STREQUAL "gfortran")
+ set(UNRES_MD_SRC0 ${UNRES_MD_SRC0} prng.f )
else()
set(UNRES_MD_SRC0 ${UNRES_MD_SRC0} prng_32.F )
endif (Fortran_COMPILER_NAME STREQUAL "ifort")
#set(FFLAGS3 "-c -w -O3 -ipo -ipo_obj -opt_report" )
set(FFLAGS3 "-w -ipo " )
elseif (Fortran_COMPILER_NAME STREQUAL "gfortran")
- set(FFLAGS0 "-I. " )
- set(FFLAGS1 "-g -I. " )
- set(FFLAGS2 "-I. ")
+ set(FFLAGS0 "-std=legacy -I. " )
+ set(FFLAGS1 "-std=legacy -g -I. " )
+ set(FFLAGS2 "-std=legacy -I. ")
#set(FFLAGS3 "-c -w -O3 -ipo -ipo_obj -opt_report" )
- set(FFLAGS3 "-I. " )
+ set(FFLAGS3 "-std=legacy -I. " )
endif (Fortran_COMPILER_NAME STREQUAL "ifort")
#=========================================
if(UNRES_MD_FF STREQUAL "GAB" )
# set preprocesor flags
- set(CPPFLAGS "PROCOR -DUNRES -DISNAN -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC" )
+ set(CPPFLAGS "PROCOR -DUNRES -DISNAN -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DSCCORPDB" )
#=========================================
# Settings for E0LL2Y force field
#=========================================
elseif(UNRES_MD_FF STREQUAL "E0LL2Y")
# set preprocesor flags
- set(CPPFLAGS "PROCOR -DUNRES -DISNAN -DSPLITELE -DLANG0" )
+ set(CPPFLAGS "PROCOR -DUNRES -DISNAN -DSPLITELE -DLANG0 -DSCCORPDB" )
endif(UNRES_MD_FF STREQUAL "GAB")
#=========================================
elseif (Fortran_COMPILER_NAME STREQUAL "gfortran")
# Add old gfortran flags
set(CPPFLAGS "${CPPFLAGS} -DG77")
+ else(Fortran_COMPILER_NAME STREQUAL "ifort")
+ # Default preprocessor flag
+ set(CPPFLAGS "${CPPFLAGS} -DPGI")
endif (Fortran_COMPILER_NAME STREQUAL "ifort")
#=========================================
endif(UNRES_WITH_MPI)
#=========================================
- # cinfo.f stupid workaround for cmake
- # - shame on me ]:)
+ # cinfo.f workaround for cmake
#=========================================
- set_property(SOURCE compinfo.c PROPERTY CMAKE_C_FLAGS "-c" )
- add_executable(compinfo-md compinfo.c)
- set_target_properties(compinfo-md PROPERTIES OUTPUT_NAME compinfo)
-
- set(UNRES_CINFO_DIR "${CMAKE_CURRENT_BINARY_DIR}" )
- add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/cinfo.f
- COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/cinfo.f ${CMAKE_CURRENT_BINARY_DIR}/cinfo.f
- COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/COMMON.IOUNITS ${CMAKE_CURRENT_BINARY_DIR}/COMMON.IOUNITS
- COMMAND ${CMAKE_CURRENT_BINARY_DIR}/compinfo | true
- DEPENDS compinfo-md )
- set_property(SOURCE ${UNRES_CINFO_DIR}/cinfo.f PROPERTY COMPILE_FLAGS ${FFLAGS0} )
+ # get the current date
+ TODAY(DATE)
+ # generate cinfo.f
+
+ set(CINFO "${CMAKE_CURRENT_BINARY_DIR}/cinfo.f")
+ FILE(WRITE ${CINFO}
+ "C CMake generated file
+ subroutine cinfo
+ include 'COMMON.IOUNITS'
+ write(iout,*)'++++ Compile info ++++'
+ write(iout,*)'Version ${UNRES_MAJOR}.${UNRES_MINOR} build ${UNRES_PATCH}'
+ ")
+
+ CINFO_FORMAT(${CINFO} "Compiled" "${DATE}" )
+ CINFO_FORMAT(${CINFO} "Compiled by" "$ENV{USER}@$ENV{HOST}" )
+ CINFO_FORMAT(${CINFO} "OS name:" "${CMAKE_SYSTEM_NAME}" )
+ CINFO_FORMAT(${CINFO} "OS release:" "${CMAKE_SYSTEM}" )
+ CINFO_FORMAT(${CINFO} "Fortran Compiler:" "${CMAKE_Fortran_COMPILER}" )
+ CINFO_FORMAT(${CINFO} "MD Force field:" "${UNRES_MD_FF}" )
+ CINFO_FORMAT(${CINFO} "CPPFLAGS =" "${CPPFLAGS}")
+
+ FILE(APPEND ${CINFO}
+ " write(iout,*)'++++ End of compile info ++++'
+ return
+ end ")
+
+ # add include path
+ set_property(SOURCE ${CMAKE_CURRENT_BINARY_DIR}/cinfo.f PROPERTY COMPILE_FLAGS "${FFLAGS0} -I${CMAKE_CURRENT_SOURCE_DIR}")
#=========================================
# Set full unres MD sources
#=========================================
- set(UNRES_MD_SRCS ${UNRES_MD_SRC0} ${UNRES_MD_SRC3} ${UNRES_CINFO_DIR}/cinfo.f )
+ set(UNRES_MD_SRCS ${UNRES_MD_SRC0} ${UNRES_MD_SRC3} ${CMAKE_CURRENT_BINARY_DIR}/cinfo.f )
#=========================================
export SIDEPAR=$DD/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k
export FOURIER=$DD/fourier_opt.parm.1igd_hc_iter3_3
export SCPPAR=$DD/scp.parm
- export SCCORPAR=$DD/rotcorr_AM1.parm
+ export SCCORPAR=$DD/sccor_pdb_shelly.dat
export PATTERN=$DD/patterns.cart
#-----------------------------------------------------------------------------
$UNRES_BIN
& dcostau,dsintau,dtauangle,dcosomicron,
& domicron
integer nterm_sccor,isccortyp,nsccortyp,nlor_sccor
- common/sccor/v1sccor(maxterm_sccor,3,20,20),
- & v2sccor(maxterm_sccor,3,20,20),
+ common/sccor/v1sccor(maxterm_sccor,3,-ntyp:ntyp,-ntyp:ntyp),
+ & v2sccor(maxterm_sccor,3,-ntyp:ntyp,-ntyp:ntyp),
+ & v0sccor(maxterm_sccor,-ntyp:ntyp,-ntyp:ntyp),
+ & nterm_sccor(-ntyp:ntyp,-ntyp:ntyp),isccortyp(-ntyp:ntyp),
+ & nsccortyp,
+ & nlor_sccor(-ntyp:ntyp,-ntyp:ntyp),
& vlor1sccor(maxterm_sccor,20,20),
& vlor2sccor(maxterm_sccor,20,20),
& vlor3sccor(maxterm_sccor,20,20),gloc_sc(3,0:maxres2,10),
+ & v0sccor(ntyp,ntyp),
& dcostau(3,3,3,maxres2),dsintau(3,3,3,maxres2),
& dtauangle(3,3,3,maxres2),dcosomicron(3,3,3,maxres2),
- & domicron(3,3,3,maxres2)
+ & domicron(3,3,3,maxres2),
+ & nterm_sccor(ntyp,ntyp),isccortyp(ntyp),nsccortyp,
+ & nlor_sccor(ntyp,ntyp)
C Calculate electrostatic (H-bonding) energy of the main chain.
C
107 continue
+ cmc
+ cmc Sep-06: egb takes care of dynamic ss bonds too
+ cmc
+ c if (dyn_ss) call dyn_set_nss
+
c print *,"Processor",myrank," computed USCSC"
#ifdef TIMING
#ifdef MPI
energia(23)=evdw_m
c print *," Processor",myrank," calls SUM_ENERGY"
call sum_energy(energia,.true.)
+ if (dyn_ss) call dyn_set_nss
c print *," Processor",myrank," left SUM_ENERGY"
#ifdef TIMING
#ifdef MPI
#ifdef SPLITELE
etot=wsc*evdw+wscp*evdw2+welec*ees+wvdwpp*evdw1
& +wang*ebe+wtor*etors+wscloc*escloc
- & +wstrain*ehpb+nss*ebr+wcorr*ecorr+wcorr5*ecorr5
+ & +wstrain*ehpb+wcorr*ecorr+wcorr5*ecorr5
& +wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3
& +wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d
& +wbond*estr+Uconst+wsccor*esccor
#else
etot=wsc*evdw+wscp*evdw2+welec*(ees+evdw1)
& +wang*ebe+wtor*etors+wscloc*escloc
- & +wstrain*ehpb+nss*ebr+wcorr*ecorr+wcorr5*ecorr5
+ & +wstrain*ehpb+wcorr*ecorr+wcorr5*ecorr5
& +wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3
& +wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d
& +wbond*estr+Uconst+wsccor*esccor
do i=1,4*nres
glocbuf(i)=gloc(i,icg)
enddo
- #define DEBUG
#ifdef DEBUG
write (iout,*) "gloc_sc before reduce"
do i=1,nres
enddo
enddo
#endif
- #undef DEBUG
do i=1,nres
do j=1,3
gloc_scbuf(j,i)=gloc_sc(j,i,icg)
call MPI_Reduce(gloc_scbuf(1,1),gloc_sc(1,1,icg),3*nres,
& MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR)
time_reduce=time_reduce+MPI_Wtime()-time00
- #define DEBUG
#ifdef DEBUG
write (iout,*) "gloc_sc after reduce"
do i=1,nres
enddo
enddo
#endif
- #undef DEBUG
#ifdef DEBUG
write (iout,*) "gloc after reduce"
do i=1,4*nres
& edihcnstr,ebr*nss,
& Uconst,etot
10 format (/'Virtual-chain energies:'//
- & 'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/
- & 'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/
- & 'EES= ',1pE16.6,' WEIGHT=',1pD16.6,' (p-p)'/
- & 'EVDWPP=',1pE16.6,' WEIGHT=',1pD16.6,' (p-p VDW)'/
- & 'ESTR= ',1pE16.6,' WEIGHT=',1pD16.6,' (stretching)'/
- & 'EBE= ',1pE16.6,' WEIGHT=',1pD16.6,' (bending)'/
- & 'ESC= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC local)'/
- & 'ETORS= ',1pE16.6,' WEIGHT=',1pD16.6,' (torsional)'/
- & 'ETORSD=',1pE16.6,' WEIGHT=',1pD16.6,' (double torsional)'/
- & 'EHPB= ',1pE16.6,' WEIGHT=',1pD16.6,
+ & 'EVDW= ',1pE16.6,' WEIGHT=',1pE16.6,' (SC-SC)'/
+ & 'EVDW2= ',1pE16.6,' WEIGHT=',1pE16.6,' (SC-p)'/
+ & 'EES= ',1pE16.6,' WEIGHT=',1pE16.6,' (p-p)'/
+ & 'EVDWPP=',1pE16.6,' WEIGHT=',1pE16.6,' (p-p VDW)'/
+ & 'ESTR= ',1pE16.6,' WEIGHT=',1pE16.6,' (stretching)'/
+ & 'EBE= ',1pE16.6,' WEIGHT=',1pE16.6,' (bending)'/
+ & 'ESC= ',1pE16.6,' WEIGHT=',1pE16.6,' (SC local)'/
+ & 'ETORS= ',1pE16.6,' WEIGHT=',1pE16.6,' (torsional)'/
+ & 'ETORSD=',1pE16.6,' WEIGHT=',1pE16.6,' (double torsional)'/
+ & 'EHPB= ',1pE16.6,' WEIGHT=',1pE16.6,
& ' (SS bridges & dist. cnstr.)'/
- & 'ECORR4=',1pE16.6,' WEIGHT=',1pD16.6,' (multi-body)'/
- & 'ECORR5=',1pE16.6,' WEIGHT=',1pD16.6,' (multi-body)'/
- & 'ECORR6=',1pE16.6,' WEIGHT=',1pD16.6,' (multi-body)'/
- & 'EELLO= ',1pE16.6,' WEIGHT=',1pD16.6,' (electrostatic-local)'/
- & 'ETURN3=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 3rd order)'/
- & 'ETURN4=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 4th order)'/
- & 'ETURN6=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 6th order)'/
- & 'ESCCOR=',1pE16.6,' WEIGHT=',1pD16.6,' (backbone-rotamer corr)'/
+ & 'ECORR4=',1pE16.6,' WEIGHT=',1pE16.6,' (multi-body)'/
+ & 'ECORR5=',1pE16.6,' WEIGHT=',1pE16.6,' (multi-body)'/
+ & 'ECORR6=',1pE16.6,' WEIGHT=',1pE16.6,' (multi-body)'/
+ & 'EELLO= ',1pE16.6,' WEIGHT=',1pE16.6,' (electrostatic-local)'/
+ & 'ETURN3=',1pE16.6,' WEIGHT=',1pE16.6,' (turns, 3rd order)'/
+ & 'ETURN4=',1pE16.6,' WEIGHT=',1pE16.6,' (turns, 4th order)'/
+ & 'ETURN6=',1pE16.6,' WEIGHT=',1pE16.6,' (turns, 6th order)'/
+ & 'ESCCOR=',1pE16.6,' WEIGHT=',1pE16.6,' (backbone-rotamer corr)'/
& 'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/
& 'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/
& 'UCONST= ',1pE16.6,' (Constraint energy)'/
c write(iout,*)'Entering ELJ nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
do i=iatsc_s,iatsc_e
- itypi=iabs(itype(i))
- itypi1=iabs(itype(i+1))
+ itypi=itype(i)
+ itypi1=itype(i+1)
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
cd write (iout,*) 'i=',i,' iint=',iint,' istart=',istart(i,iint),
cd & 'iend=',iend(i,iint)
do j=istart(i,iint),iend(i,iint)
- itypj=iabs(itype(j))
+ itypj=itype(j)
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
zj=c(3,nres+j)-zi
c print *,'Entering ELJK nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
do i=iatsc_s,iatsc_e
- itypi=iabs(itype(i))
- itypi1=iabs(itype(i+1))
+ itypi=itype(i)
+ itypi1=itype(i+1)
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
C
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
- itypj=iabs(itype(j))
+ itypj=itype(j)
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
zj=c(3,nres+j)-zi
c endif
ind=0
do i=iatsc_s,iatsc_e
- itypi=iabs(itype(i))
- itypi1=iabs(itype(i+1))
+ itypi=itype(i)
+ itypi1=itype(i+1)
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
ind=ind+1
- itypj=itype(j)
+ itypj=iabs(itype(j))
c dscj_inv=dsc_inv(itypj)
dscj_inv=vbld_inv(j+nres)
chi1=chi(itypi,itypj)
include 'COMMON.IOUNITS'
include 'COMMON.CALC'
include 'COMMON.CONTROL'
+ include 'COMMON.SBRIDGE'
logical lprn
evdw=0.0D0
ccccc energy_dec=.false.
c if (icall.eq.0) lprn=.false.
ind=0
do i=iatsc_s,iatsc_e
- itypi=iabs(itype(i))
- itypi1=iabs(itype(i+1))
+ itypi=itype(i)
+ itypi1=itype(i+1)
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
C
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
+ IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN
+ call dyn_ssbond_ene(i,j,evdwij)
+ evdw=evdw+evdwij
+ if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)')
+ & 'evdw',i,j,evdwij,' ss'
+ ELSE
ind=ind+1
- itypj=iabs(itype(j))
+ itypj=itype(j)
c dscj_inv=dsc_inv(itypj)
dscj_inv=vbld_inv(j+nres)
c write (iout,*) "j",j,dsc_inv(itypj),dscj_inv,
#else
call sc_grad
#endif
+ ENDIF ! dyn_ss
enddo ! j
enddo ! iint
enddo ! i
c if (icall.eq.0) lprn=.true.
ind=0
do i=iatsc_s,iatsc_e
- itypi=iabs(itype(i))
- itypi1=iabs(itype(i+1))
+ itypi=itype(i)
+ itypi1=itype(i+1)
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
ind=ind+1
- itypj=iabs(itype(j))
+ itypj=itype(j)
c dscj_inv=dsc_inv(itypj)
dscj_inv=vbld_inv(j+nres)
sig0ij=sigma(itypi,itypj)
cd print *,'Entering Esoft_sphere nnt=',nnt,' nct=',nct
evdw=0.0D0
do i=iatsc_s,iatsc_e
- itypi=iabs(itype(i))
- itypi1=iabs(itype(i+1))
+ itypi=itype(i)
+ itypi1=itype(i+1)
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
cd write (iout,*) 'i=',i,' iint=',iint,' istart=',istart(i,iint),
cd & 'iend=',iend(i,iint)
do j=istart(i,iint),iend(i,iint)
- itypj=iabs(itype(j))
+ itypj=itype(j)
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
zj=c(3,nres+j)-zi
do iint=1,nscp_gr(i)
do j=iscpstart(i,iint),iscpend(i,iint)
- itypj=iabs(itype(j))
+ itypj=itype(j)
C Uncomment following three lines for SC-p interactions
c xj=c(1,nres+j)-xi
c yj=c(2,nres+j)-yi
do iint=1,nscp_gr(i)
do j=iscpstart(i,iint),iscpend(i,iint)
- itypj=iabs(itype(j))
+ itypj=itype(j)
C Uncomment following three lines for SC-p interactions
c xj=c(1,nres+j)-xi
c yj=c(2,nres+j)-yi
c & dhpb(i),dhpb1(i),forcon(i)
C 24/11/03 AL: SS bridges handled separately because of introducing a specific
C distance and angle dependent SS bond potential.
- if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and. iabs(itype(jjj
- &)).eq.1) then
+ cmc if (ii.gt.nres .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then
+ C 18/07/06 MC: Use the convention that the first nss pairs are SS bonds
+ if (.not.dyn_ss .and. i.le.nss) then
+ C 15/02/13 CC dynamic SSbond - additional check
+ if (ii.gt.nres
+ & .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then
call ssbond_ene(iii,jjj,eij)
ehpb=ehpb+2*eij
+ endif
cd write (iout,*) "eij",eij
else if (ii.gt.nres .and. jj.gt.nres) then
c Restraints from contact prediction
include 'COMMON.VAR'
include 'COMMON.IOUNITS'
double precision erij(3),dcosom1(3),dcosom2(3),gg(3)
- itypi=iabs(itype(i))
+ itypi=itype(i)
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
dzi=dc_norm(3,nres+i)
c dsci_inv=dsc_inv(itypi)
dsci_inv=vbld_inv(nres+i)
- itypj=iabs(itype(j))
+ itypj=itype(j)
c dscj_inv=dsc_inv(itypj)
dscj_inv=vbld_inv(nres+j)
xj=c(1,nres+j)-xi
deltat12=om2-om1+2.0d0
cosphi=om12-om1*om2
eij=akcm*deltad*deltad+akth*(deltat1*deltat1+deltat2*deltat2)
- & +akct*deltad*deltat12
+ & +akct*deltad*deltat12+ebr
& +v1ss*cosphi+v2ss*cosphi*cosphi+v3ss*cosphi*cosphi*cosphi
c write(iout,*) i,j,"rij",rij,"d0cm",d0cm," akcm",akcm," akth",akth,
c & " akct",akct," deltad",deltad," deltat",deltat1,deltat2,
c 09/18/07 AL: multimodal bond potential based on AM1 CA-SC PMF's included
c
do i=ibond_start,ibond_end
- iti=iabs(itype(i))
+ iti=itype(i)
if (iti.ne.10) then
nbi=nbondterm(iti)
if (nbi.eq.1) then
do i=ithet_start,ithet_end
C Zero the energy function and its derivative at 0 or pi.
call splinthet(theta(i),0.5d0*delta,ss,ssd)
- it=(itype(i-1))
- ichir1=isign(1,itype(i-2))
- ichir2=isign(1,itype(i))
- if (itype(i-2).eq.10) ichir1=isign(1,itype(i-1))
- if (itype(i).eq.10) ichir2=isign(1,itype(i-1))
- if (itype(i-1).eq.10) then
- itype1=isign(10,itype(i-2))
- ichir11=isign(1,itype(i-2))
- ichir12=isign(1,itype(i-2))
- itype2=isign(10,itype(i))
- ichir21=isign(1,itype(i))
- ichir22=isign(1,itype(i))
- endif
+ it=itype(i-1)
if (i.gt.3) then
#ifdef OSF
phii=phi(i)
C In following comments this theta will be referred to as t_c.
thet_pred_mean=0.0d0
do k=1,2
- athetk=athet(k,it,ichir1,ichir2)
- bthetk=bthet(k,it,ichir1,ichir2)
- if (it.eq.10) then
- athetk=athet(k,itype1,ichir11,ichir12)
- bthetk=bthet(k,itype2,ichir21,ichir22)
- endif
+ athetk=athet(k,it)
+ bthetk=bthet(k,it)
thet_pred_mean=thet_pred_mean+athetk*y(k)+bthetk*z(k)
enddo
dthett=thet_pred_mean*ssd
thet_pred_mean=thet_pred_mean*ss+a0thet(it)
C Derivatives of the "mean" values in gamma1 and gamma2.
- dthetg1=(-athet(1,it,ichir1,ichir2)*y(2)
- &+athet(2,it,ichir1,ichir2)*y(1))*ss
- dthetg2=(-bthet(1,it,ichir1,ichir2)*z(2)
- & +bthet(2,it,ichir1,ichir2)*z(1))*ss
- if (it.eq.10) then
- dthetg1=(-athet(1,itype1,ichir11,ichir12)*y(2)
- &+athet(2,itype1,ichir11,ichir12)*y(1))*ss
- dthetg2=(-bthet(1,itype2,ichir21,ichir22)*z(2)
- & +bthet(2,itype2,ichir21,ichir22)*z(1))*ss
- endif
+ dthetg1=(-athet(1,it)*y(2)+athet(2,it)*y(1))*ss
+ dthetg2=(-bthet(1,it)*z(2)+bthet(2,it)*z(1))*ss
if (theta(i).gt.pi-delta) then
call theteng(pi-delta,thet_pred_mean,theta0(it),f0,fprim0,
& E_tc0)
enddo
endif
if (i.lt.nres) then
+
+ if (iabs(itype(i+1)).eq.20) iblock=2
+ if (iabs(itype(i+1)).ne.20) iblock=1
#ifdef OSF
phii1=phi(i+1)
if (phii1.ne.phii1) phii1=150.0
sinph2(k)=0.0d0
enddo
endif
- ethetai=aa0thet(ityp1,ityp2,ityp3)
+ ethetai=aa0thet(ityp1,ityp2,ityp3,iblock)
do k=1,ndouble
do l=1,k-1
ccl=cosph1(l)*cosph2(k-l)
enddo
endif
do k=1,ntheterm
- ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3)*sinkt(k)
- dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3)
+ ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3,iblock)*sinkt(k)
+ dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3,iblock)
& *coskt(k)
if (lprn)
- & write (iout,*) "k",k," aathet",aathet(k,ityp1,ityp2,ityp3),
+ & write (iout,*) "k",k,
+ & "aathet",aathet(k,ityp1,ityp2,ityp3,iblock),
& " ethetai",ethetai
enddo
if (lprn) then
endif
do m=1,ntheterm2
do k=1,nsingle
- aux=bbthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)
- & +ccthet(k,m,ityp1,ityp2,ityp3)*sinph1(k)
- & +ddthet(k,m,ityp1,ityp2,ityp3)*cosph2(k)
- & +eethet(k,m,ityp1,ityp2,ityp3)*sinph2(k)
+ aux=bbthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k)
+ & +ccthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k)
+ & +ddthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k)
+ & +eethet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k)
ethetai=ethetai+sinkt(m)*aux
dethetai=dethetai+0.5d0*m*aux*coskt(m)
dephii=dephii+k*sinkt(m)*(
- & ccthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)-
- & bbthet(k,m,ityp1,ityp2,ityp3)*sinph1(k))
+ & ccthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k)-
+ & bbthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k))
dephii1=dephii1+k*sinkt(m)*(
- & eethet(k,m,ityp1,ityp2,ityp3)*cosph2(k)-
- & ddthet(k,m,ityp1,ityp2,ityp3)*sinph2(k))
+ & eethet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k)-
+ & ddthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k))
if (lprn)
& write (iout,*) "m",m," k",k," bbthet",
- & bbthet(k,m,ityp1,ityp2,ityp3)," ccthet",
- & ccthet(k,m,ityp1,ityp2,ityp3)," ddthet",
- & ddthet(k,m,ityp1,ityp2,ityp3)," eethet",
- & eethet(k,m,ityp1,ityp2,ityp3)," ethetai",ethetai
+ & bbthet(k,m,ityp1,ityp2,ityp3,iblock)," ccthet",
+ & ccthet(k,m,ityp1,ityp2,ityp3,iblock)," ddthet",
+ & ddthet(k,m,ityp1,ityp2,ityp3,iblock)," eethet",
+ & eethet(k,m,ityp1,ityp2,ityp3,iblock)," ethetai",ethetai
enddo
enddo
if (lprn)
do m=1,ntheterm3
do k=2,ndouble
do l=1,k-1
- aux=ffthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)
+ aux=ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)
+
ethetai=ethetai+sinkt(m)*aux
dethetai=dethetai+0.5d0*m*coskt(m)*aux
dephii=dephii+l*sinkt(m)*(
- & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)-
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+ & -ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)-
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l))
+
dephii1=dephii1+(k-l)*sinkt(m)*(
- & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)-
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+ &-ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)-
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l))
+
if (lprn) then
write (iout,*) "m",m," k",k," l",l," ffthet",
- & ffthet(l,k,m,ityp1,ityp2,ityp3),
- & ffthet(k,l,m,ityp1,ityp2,ityp3)," ggthet",
- & ggthet(l,k,m,ityp1,ityp2,ityp3),
- & ggthet(k,l,m,ityp1,ityp2,ityp3)," ethetai",ethetai
+ & ffthet(l,k,m,ityp1,ityp2,ityp3,iblock),
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)," ggthet",
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock),
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock),
+ & " ethetai",ethetai
+
write (iout,*) cosph1ph2(l,k)*sinkt(m),
& cosph1ph2(k,l)*sinkt(m),
& sinph1ph2(l,k)*sinkt(m),sinph1ph2(k,l)*sinkt(m)
do i=loc_start,loc_end
it=itype(i)
if (it.eq.10) goto 1
- nlobit=nlob(iabs(it))
+ nlobit=nlob(it)
c print *,'i=',i,' it=',it,' nlobit=',nlobit
c write (iout,*) 'i=',i,' ssa=',ssa,' ssad=',ssad
theti=theta(i+1)-pipol
do j=1,nlobit
#ifdef OSF
- adexp=bsc(j,iabs(it))-0.5D0*contr(j,iii)+emin
+ adexp=bsc(j,it)-0.5D0*contr(j,iii)+emin
if(adexp.ne.adexp) adexp=1.0
expfac=dexp(adexp)
#else
- expfac=dexp(bsc(j,iabs(it))-0.5D0*contr(j,iii)+emin)
+ expfac=dexp(bsc(j,it)-0.5D0*contr(j,iii)+emin)
#endif
cd print *,'j=',j,' expfac=',expfac
escloc_i=escloc_i+expfac
dersc12=0.0d0
do j=1,nlobit
- expfac=dexp(bsc(j,iabs(it))-0.5D0*contr(j)+emin)
+ expfac=dexp(bsc(j,it)-0.5D0*contr(j)+emin)
escloc_i=escloc_i+expfac
do k=1,2
dersc(k)=dersc(k)+Ax(k,j)*expfac
cosfac=dsqrt(cosfac2)
sinfac2=0.5d0/(1.0d0-costtab(i+1))
sinfac=dsqrt(sinfac2)
- it=itype(i)
+ it=iabs(itype(i))
if (it.eq.10) goto 1
c
C Compute the axes of tghe local cartesian coordinates system; store in
y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
enddo
do j = 1,3
- z_prime(j) = -uz(j,i-1)
+ z_prime(j) = -uz(j,i-1)*dsign(1.0d0,dfloat(itype(i)))
enddo
c write (2,*) "i",i
c write (2,*) "x_prime",(x_prime(j),j=1,3)
C Compute the energy of the ith side cbain
C
c write (2,*) "xx",xx," yy",yy," zz",zz
- it=itype(i)
+ it=iabs(itype(i))
do j = 1,65
x(j) = sc_parmin(j,it)
enddo
Cc diagnostics - remove later
xx1 = dcos(alph(2))
yy1 = dsin(alph(2))*dcos(omeg(2))
- zz1 = -dsin(alph(2))*dsin(omeg(2))
+ zz1 = -dsign(1.0, dfloat(itype(i)))*dsin(alph(2))*dsin(omeg(2))
write(2,'(3f8.1,3f9.3,1x,3f9.3)')
& alph(2)*rad2deg,omeg(2)*rad2deg,theta(3)*rad2deg,xx,yy,zz,
& xx1,yy1,zz1
dZZ_Ci1(k)=0.0d0
dZZ_Ci(k)=0.0d0
do j=1,3
- dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)*dC_norm(j,i+nres)
- dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)*dC_norm(j,i+nres)
+ dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)
+ & *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres)
+ dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)
+ & *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres)
enddo
dXX_XYZ(k)=vbld_inv(i+nres)*(x_prime(k)-xx*dC_norm(k,i+nres))
etors=0.0D0
do i=iphi_start,iphi_end
etors_ii=0.0D0
+c if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1
+c & .or. itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
itori=itortyp(itype(i-2))
itori1=itortyp(itype(i-1))
phii=phi(i)
gloci=0.0D0
C Regular cosine and sine terms
- do j=1,nterm(itori,itori1,iblock)
- v1ij=v1(j,itori,itori1,iblock)
- v2ij=v2(j,itori,itori1,iblock)
+ do j=1,nterm(itori,itori1)
+ v1ij=v1(j,itori,itori1)
+ v2ij=v2(j,itori,itori1)
cosphi=dcos(j*phii)
sinphi=dsin(j*phii)
etors=etors+v1ij*cosphi+v2ij*sinphi
C
cosphi=dcos(0.5d0*phii)
sinphi=dsin(0.5d0*phii)
- do j=1,nlor(itori,itori1,iblock)
+ do j=1,nlor(itori,itori1)
vl1ij=vlor1(j,itori,itori1)
vl2ij=vlor2(j,itori,itori1)
vl3ij=vlor3(j,itori,itori1)
gloci=gloci+vl1ij*(vl3ij*cosphi-vl2ij*sinphi)*pom
enddo
C Subtract the constant term
- etors=etors-v0(itori,itori1,iblock)
+ etors=etors-v0(itori,itori1)
if (energy_dec) write (iout,'(a6,i5,0pf7.3)')
- & 'etor',i,etors_ii-v0(itori,itori1,iblock)
+ & 'etor',i,etors_ii-v0(itori,itori1)
if (lprn)
& write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)')
& restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
- & (v1(j,itori,itori1,iblock),j=1,6),
- & (v2(j,itori,itori1,iblock),j=1,6)
+ & (v1(j,itori,itori1),j=1,6),(v2(j,itori,itori1),j=1,6)
gloc(i-3,icg)=gloc(i-3,icg)+wtor*gloci
c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg)
enddo
c lprn=.true.
etors_d=0.0D0
do i=iphid_start,iphid_end
+c if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1
+c & .or. itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
itori=itortyp(itype(i-2))
itori1=itortyp(itype(i-1))
itori2=itortyp(itype(i))
- iblock=1
- if (iabs(itype(i+1)).eq.20) iblock=2
phii=phi(i)
phii1=phi(i+1)
gloci1=0.0D0
gloci2=0.0D0
- do j=1,ntermd_1(itori,itori1,itori2,iblock)
- v1cij=v1c(1,j,itori,itori1,itori2,iblock)
- v1sij=v1s(1,j,itori,itori1,itori2,iblock)
- v2cij=v1c(2,j,itori,itori1,itori2,iblock)
- v2sij=v1s(2,j,itori,itori1,itori2,iblock)
+ do j=1,ntermd_1(itori,itori1,itori2)
+ v1cij=v1c(1,j,itori,itori1,itori2)
+ v1sij=v1s(1,j,itori,itori1,itori2)
+ v2cij=v1c(2,j,itori,itori1,itori2)
+ v2sij=v1s(2,j,itori,itori1,itori2)
cosphi1=dcos(j*phii)
sinphi1=dsin(j*phii)
cosphi2=dcos(j*phii1)
gloci1=gloci1+j*(v1sij*cosphi1-v1cij*sinphi1)
gloci2=gloci2+j*(v2sij*cosphi2-v2cij*sinphi2)
enddo
- do k=2,ntermd_2(itori,itori1,itori2,iblock)
+ do k=2,ntermd_2(itori,itori1,itori2)
do l=1,k-1
- v1cdij = v2c(k,l,itori,itori1,itori2,iblock)
- v2cdij = v2c(l,k,itori,itori1,itori2,iblock)
- v1sdij = v2s(k,l,itori,itori1,itori2,iblock)
- v2sdij = v2s(l,k,itori,itori1,itori2,iblock)
+ v1cdij = v2c(k,l,itori,itori1,itori2)
+ v2cdij = v2c(l,k,itori,itori1,itori2)
+ v1sdij = v2s(k,l,itori,itori1,itori2)
+ v2sdij = v2s(l,k,itori,itori1,itori2)
cosphi1p2=dcos(l*phii+(k-l)*phii1)
cosphi1m2=dcos(l*phii-(k-l)*phii1)
sinphi1p2=dsin(l*phii+(k-l)*phii1)
C Set lprn=.true. for debugging
lprn=.false.
c lprn=.true.
-c write (iout,*) "EBACK_SC_COR",iphi_start,iphi_end,nterm_sccor
+c write (iout,*) "EBACK_SC_COR",itau_start,itau_end
esccor=0.0D0
do i=itau_start,itau_end
esccor_ii=0.0D0
+ if ((itype(i-2).eq.ntyp1).or.(itype(i-1).eq.ntyp1)) cycle
isccori=isccortyp(itype(i-2))
isccori1=isccortyp(itype(i-1))
phii=phi(i)
c 3 = SC...Ca...Ca...SCi
gloci=0.0D0
if (((intertyp.eq.3).and.((itype(i-2).eq.10).or.
- & (itype(i-1).eq.10).or.(itype(i-2).eq.21).or.
- & (itype(i-1).eq.21)))
+ & (itype(i-1).eq.10).or.(itype(i-2).eq.ntyp1).or.
+ & (itype(i-1).eq.ntyp1)))
& .or. ((intertyp.eq.1).and.((itype(i-2).eq.10)
- & .or.(itype(i-2).eq.21)))
+ & .or.(itype(i-2).eq.ntyp1).or.(itype(i-1).eq.ntyp1)
+ & .or.(itype(i).eq.ntyp1)))
& .or.((intertyp.eq.2).and.((itype(i-1).eq.10).or.
- & (itype(i-1).eq.21)))) cycle
- if ((intertyp.eq.2).and.(i.eq.4).and.(itype(1).eq.21)) cycle
- if ((intertyp.eq.1).and.(i.eq.nres).and.(itype(nres).eq.21))
+ & (itype(i-1).eq.ntyp1).or.(itype(i-2).eq.ntyp1).or.
+ & (itype(i-3).eq.ntyp1)))) cycle
+ if ((intertyp.eq.2).and.(i.eq.4).and.(itype(1).eq.ntyp1)) cycle
+ if ((intertyp.eq.1).and.(i.eq.nres).and.(itype(nres).eq.ntyp1))
& cycle
do j=1,nterm_sccor(isccori,isccori1)
v1ij=v1sccor(j,intertyp,isccori,isccori1)
c &gloc_sc(intertyp,i-3,icg)
if (lprn)
& write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)')
- & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
- & (v1sccor(j,intertyp,itori,itori1),j=1,6)
- & ,(v2sccor(j,intertyp,itori,itori1),j=1,6)
+ & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,isccori,isccori1,
+ & (v1sccor(j,intertyp,isccori,isccori1),j=1,6)
+ & ,(v2sccor(j,intertyp,isccori,isccori1),j=1,6)
gsccor_loc(i-3)=gsccor_loc(i-3)+gloci
enddo !intertyp
enddo
include 'COMMON.GEO'
logical swap
double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2),
- & auxvec1(2),auxvec2(1),auxmat1(2,2)
+ & auxvec1(2),auxvec2(2),auxmat1(2,2)
logical lprn
common /kutas/ lprn
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
include 'COMMON.SETUP'
character*1 t1,t2,t3
character*1 onelett(4) /"G","A","P","D"/
- character*1 toronelet(-2:2) /"p","a","G","A","P"/
logical lprint,LaTeX
dimension blower(3,3,maxlob)
dimension b(13)
C of the virtual-bond valence angles theta
C
do i=1,ntyp
- read (ithep,*,err=111,end=111) a0thet(i),(athet(j,i,1,1),j=1,2),
- & (bthet(j,i,1,1),j=1,2)
+ read (ithep,*,err=111,end=111) a0thet(i),(athet(j,i),j=1,2),
+ & (bthet(j,i),j=1,2)
read (ithep,*,err=111,end=111) (polthet(j,i),j=0,3)
read (ithep,*,err=111,end=111) (gthet(j,i),j=1,3)
read (ithep,*,err=111,end=111) theta0(i),sig0(i),sigc0(i)
sigc0(i)=sigc0(i)**2
enddo
- do i=1,ntyp
- athet(1,i,1,-1)=athet(1,i,1,1)
- athet(2,i,1,-1)=athet(2,i,1,1)
- bthet(1,i,1,-1)=-bthet(1,i,1,1)
- bthet(2,i,1,-1)=-bthet(2,i,1,1)
- athet(1,i,-1,1)=-athet(1,i,1,1)
- athet(2,i,-1,1)=-athet(2,i,1,1)
- bthet(1,i,-1,1)=bthet(1,i,1,1)
- bthet(2,i,-1,1)=bthet(2,i,1,1)
- enddo
- do i=-ntyp,-1
- a0thet(i)=a0thet(-i)
- athet(1,i,-1,-1)=athet(1,-i,1,1)
- athet(2,i,-1,-1)=-athet(2,-i,1,1)
- bthet(1,i,-1,-1)=bthet(1,-i,1,1)
- bthet(2,i,-1,-1)=-bthet(2,-i,1,1)
- athet(1,i,-1,1)=athet(1,-i,1,1)
- athet(2,i,-1,1)=-athet(2,-i,1,1)
- bthet(1,i,-1,1)=-bthet(1,-i,1,1)
- bthet(2,i,-1,1)=bthet(2,-i,1,1)
- athet(1,i,1,-1)=-athet(1,-i,1,1)
- athet(2,i,1,-1)=athet(2,-i,1,1)
- bthet(1,i,1,-1)=bthet(1,-i,1,1)
- bthet(2,i,1,-1)=-bthet(2,-i,1,1)
- theta0(i)=theta0(-i)
- sig0(i)=sig0(-i)
- sigc0(i)=sigc0(-i)
- do j=0,3
- polthet(j,i)=polthet(j,-i)
- enddo
- do j=1,3
- gthet(j,i)=gthet(j,-i)
- enddo
- enddo
close (ithep)
if (lprint) then
if (.not.LaTeX) then
& ' B1 ',' B2 '
do i=1,ntyp
write(iout,'(a3,i4,2x,5(1pe14.5))') restyp(i),i,
- & a0thet(i),(athet(j,i,1,1),j=1,2),(bthet(j,i,1,1),j=1,2)
+ & a0thet(i),(athet(j,i),j=1,2),(bthet(j,i),j=1,2)
enddo
write (iout,'(/a/9x,5a/79(1h-))')
& 'Parameters of the expression for sigma(theta_c):',
& ' b1*10^1 ',' b2*10^1 '
do i=1,ntyp
write(iout,'(a3,1h&,2x,5(f8.3,1h&))') restyp(i),
- & a0thet(i),(100*athet(j,i,1,1),j=1,2),
- & (10*bthet(j,i,1,1),j=1,2)
+ & a0thet(i),(100*athet(j,i),j=1,2),(10*bthet(j,i),j=1,2)
enddo
write (iout,'(/a/9x,5a/79(1h-))')
& 'Parameters of the expression for sigma(theta_c):',
& ntheterm3,nsingle,ndouble
nntheterm=max0(ntheterm,ntheterm2,ntheterm3)
read (ithep,*,err=111,end=111) (ithetyp(i),i=1,ntyp1)
- do i=1,maxthetyp
- do j=1,maxthetyp
- do k=1,maxthetyp
- aa0thet(i,j,k)=0.0d0
+ do i=-ntyp1,-1
+ ithetyp(i)=-ithetyp(-i)
+ enddo
+ do iblock=1,2
+ do i=-maxthetyp,maxthetyp
+ do j=-maxthetyp,maxthetyp
+ do k=-maxthetyp,maxthetyp
+ aa0thet(i,j,k,iblock)=0.0d0
do l=1,ntheterm
- aathet(l,i,j,k)=0.0d0
+ aathet(l,i,j,k,iblock)=0.0d0
enddo
do l=1,ntheterm2
do m=1,nsingle
- bbthet(m,l,i,j,k)=0.0d0
- ccthet(m,l,i,j,k)=0.0d0
- ddthet(m,l,i,j,k)=0.0d0
- eethet(m,l,i,j,k)=0.0d0
+ bbthet(m,l,i,j,k,iblock)=0.0d0
+ ccthet(m,l,i,j,k,iblock)=0.0d0
+ ddthet(m,l,i,j,k,iblock)=0.0d0
+ eethet(m,l,i,j,k,iblock)=0.0d0
enddo
enddo
do l=1,ntheterm3
do m=1,ndouble
do mm=1,ndouble
- ffthet(mm,m,l,i,j,k)=0.0d0
- ggthet(mm,m,l,i,j,k)=0.0d0
+ ffthet(mm,m,l,i,j,k,iblock)=0.0d0
+ ggthet(mm,m,l,i,j,k,iblock)=0.0d0
enddo
enddo
enddo
enddo
enddo
- enddo
- do i=1,nthetyp
- do j=1,nthetyp
- do k=1,nthetyp
- read (ithep,'(3a)',end=111,err=111) res1,res2,res3
- read (ithep,*,end=111,err=111) aa0thet(i,j,k)
- read (ithep,*,end=111,err=111)(aathet(l,i,j,k),l=1,ntheterm)
+ enddo
+ enddo
+c VAR:iblock means terminally blocking group 1=non-proline 2=proline
+ do iblock=1,2
+c VAR:ntethtyp is type of theta potentials type currently 0=glycine
+c VAR:1=non-glicyne non-proline 2=proline
+c VAR:negative values for D-aminoacid
+ do i=0,nthetyp
+ do j=-nthetyp,nthetyp
+ do k=-nthetyp,nthetyp
+ read (ithep,'(6a)',end=111,err=111) res1
+c VAR: aa0thet is variable describing the average value of Foureir
+c VAR: expansion series
+ read (ithep,*,end=111,err=111) aa0thet(i,j,k,iblock)
+c VAR: aathet is foureir expansion in theta/2 angle for full formula
+c VAR: look at the fitting equation in Kozlowska et al., J. Phys.:
+Condens. Matter 19 (2007) 285203 and Sieradzan et al., unpublished
+ read (ithep,*,end=111,err=111)
+ &(aathet(l,i,j,k,iblock),l=1,ntheterm)
read (ithep,*,end=111,err=111)
- & ((bbthet(lll,ll,i,j,k),lll=1,nsingle),
- & (ccthet(lll,ll,i,j,k),lll=1,nsingle),
- & (ddthet(lll,ll,i,j,k),lll=1,nsingle),
- & (eethet(lll,ll,i,j,k),lll=1,nsingle),ll=1,ntheterm2)
+ & ((bbthet(lll,ll,i,j,k,iblock),lll=1,nsingle),
+ & (ccthet(lll,ll,i,j,k,iblock),lll=1,nsingle),
+ & (ddthet(lll,ll,i,j,k,iblock),lll=1,nsingle),
+ & (eethet(lll,ll,i,j,k,iblock),lll=1,nsingle),
+ & ll=1,ntheterm2)
read (ithep,*,end=111,err=111)
- & (((ffthet(llll,lll,ll,i,j,k),ffthet(lll,llll,ll,i,j,k),
- & ggthet(llll,lll,ll,i,j,k),ggthet(lll,llll,ll,i,j,k),
+ & (((ffthet(llll,lll,ll,i,j,k,iblock),
+ & ffthet(lll,llll,ll,i,j,k,iblock),
+ & ggthet(llll,lll,ll,i,j,k,iblock),
+ & ggthet(lll,llll,ll,i,j,k,iblock),
& llll=1,lll-1),lll=2,ndouble),ll=1,ntheterm3)
enddo
enddo
enddo
+
+
C
C For dummy ends assign glycine-type coefficients of theta-only terms; the
C coefficients of theta-and-gamma-dependent terms are zero.
-C
+C IF YOU WANT VALENCE POTENTIALS FOR DUMMY ATOM UNCOMENT BELOW (NOT
+C RECOMENTDED AFTER VERSION 3.3)
+c do i=1,nthetyp
+c do j=1,nthetyp
+c do l=1,ntheterm
+c aathet(l,i,j,nthetyp+1,iblock)=aathet(l,i,j,1,iblock)
+c aathet(l,nthetyp+1,i,j,iblock)=aathet(l,1,i,j,iblock)
+c enddo
+c aa0thet(i,j,nthetyp+1,iblock)=aa0thet(i,j,1,iblock)
+c aa0thet(nthetyp+1,i,j,iblock)=aa0thet(1,i,j,iblock)
+c enddo
+c do l=1,ntheterm
+c aathet(l,nthetyp+1,i,nthetyp+1,iblock)=aathet(l,1,i,1,iblock)
+c enddo
+c aa0thet(nthetyp+1,i,nthetyp+1,iblock)=aa0thet(1,i,1,iblock)
+c enddo
+c enddo
+C AND COMMENT THE LOOPS BELOW
do i=1,nthetyp
do j=1,nthetyp
do l=1,ntheterm
- aathet(l,i,j,nthetyp+1)=aathet(l,i,j,1)
- aathet(l,nthetyp+1,i,j)=aathet(l,1,i,j)
+ aathet(l,i,j,nthetyp+1,iblock)=0.0d0
+ aathet(l,nthetyp+1,i,j,iblock)=0.0d0
enddo
- aa0thet(i,j,nthetyp+1)=aa0thet(i,j,1)
- aa0thet(nthetyp+1,i,j)=aa0thet(1,i,j)
+ aa0thet(i,j,nthetyp+1,iblock)=0.0d0
+ aa0thet(nthetyp+1,i,j,iblock)=0.0d0
enddo
do l=1,ntheterm
- aathet(l,nthetyp+1,i,nthetyp+1)=aathet(l,1,i,1)
+ aathet(l,nthetyp+1,i,nthetyp+1,iblock)=0.0d0
enddo
- aa0thet(nthetyp+1,i,nthetyp+1)=aa0thet(1,i,1)
+ aa0thet(nthetyp+1,i,nthetyp+1,iblock)=0.0d0
enddo
+ enddo
+C TILL HERE
+C Substitution for D aminoacids from symmetry.
+ do iblock=1,2
+ do i=-nthetyp,0
+ do j=-nthetyp,nthetyp
+ do k=-nthetyp,nthetyp
+ aa0thet(i,j,k,iblock)=aa0thet(-i,-j,-k,iblock)
+ do l=1,ntheterm
+ aathet(l,i,j,k,iblock)=aathet(l,-i,-j,-k,iblock)
+ enddo
+ do ll=1,ntheterm2
+ do lll=1,nsingle
+ bbthet(lll,ll,i,j,k,iblock)=bbthet(lll,ll,-i,-j,-k,iblock)
+ ccthet(lll,ll,i,j,k,iblock)=-ccthet(lll,ll,-i,-j,-k,iblock)
+ ddthet(lll,ll,i,j,k,iblock)=ddthet(lll,ll,-i,-j,-k,iblock)
+ eethet(lll,ll,i,j,k,iblock)=-eethet(lll,ll,-i,-j,-k,iblock)
+ enddo
+ enddo
+ do ll=1,ntheterm3
+ do lll=2,ndouble
+ do llll=1,lll-1
+ ffthet(llll,lll,ll,i,j,k,iblock)=
+ & ffthet(llll,lll,ll,-i,-j,-k,iblock)
+ ffthet(lll,llll,ll,i,j,k,iblock)=
+ & ffthet(lll,llll,ll,-i,-j,-k,iblock)
+ ggthet(llll,lll,ll,i,j,k,iblock)=
+ & -ggthet(llll,lll,ll,-i,-j,-k,iblock)
+ ggthet(lll,llll,ll,i,j,k,iblock)=
+ & -ggthet(lll,llll,ll,-i,-j,-k,iblock)
+ enddo !ll
+ enddo !lll
+ enddo !llll
+ enddo !k
+ enddo !j
+ enddo !i
+ enddo !iblock
C
C Control printout of the coefficients of virtual-bond-angle potentials
C
do i=1,nthetyp+1
do j=1,nthetyp+1
do k=1,nthetyp+1
- write (iout,'(//4a)')
- & 'Type ',onelett(i),onelett(j),onelett(k)
+ write (iout,'(//4a)')
+ & 'Type ',onelett(i),onelett(j),onelett(k)
write (iout,'(//a,10x,a)') " l","a[l]"
- write (iout,'(i2,1pe15.5)') 0,aa0thet(i,j,k)
+ write (iout,'(i2,1pe15.5)') 0,aa0thet(i,j,k,iblock)
write (iout,'(i2,1pe15.5)')
- & (l,aathet(l,i,j,k),l=1,ntheterm)
+ & (l,aathet(l,i,j,k,iblock),l=1,ntheterm)
do l=1,ntheterm2
- write (iout,'(//2h m,4(9x,a,3h[m,,i1,1h]))')
+ write (iout,'(//2h m,4(9x,a,3h[m,,i1,1h]))')
& "b",l,"c",l,"d",l,"e",l
do m=1,nsingle
write (iout,'(i2,4(1pe15.5))') m,
- & bbthet(m,l,i,j,k),ccthet(m,l,i,j,k),
- & ddthet(m,l,i,j,k),eethet(m,l,i,j,k)
+ & bbthet(m,l,i,j,k,iblock),ccthet(m,l,i,j,k,iblock),
+ & ddthet(m,l,i,j,k,iblock),eethet(m,l,i,j,k,iblock)
enddo
enddo
do l=1,ntheterm3
do m=2,ndouble
do n=1,m-1
write (iout,'(i1,1x,i1,4(1pe15.5))') n,m,
- & ffthet(n,m,l,i,j,k),ffthet(m,n,l,i,j,k),
- & ggthet(n,m,l,i,j,k),ggthet(m,n,l,i,j,k)
+ & ffthet(n,m,l,i,j,k,iblock),
+ & ffthet(m,n,l,i,j,k,iblock),
+ & ggthet(n,m,l,i,j,k,iblock),
+ & ggthet(m,n,l,i,j,k,iblock)
enddo
enddo
enddo
endif
write (2,*) "Start reading THETA_PDB"
do i=1,ntyp
- read (ithep_pdb,*,err=111,end=111) a0thet(i),(athet(j,i),j=1,2),
- & (bthet(j,i),j=1,2)
+ read (ithep_pdb,*,err=111,end=111)
+ & a0thet(i),(athet(j,i,1,1),j=1,2),
+ & (bthet(j,i,1,1),j=1,2)
read (ithep_pdb,*,err=111,end=111) (polthet(j,i),j=0,3)
read (ithep_pdb,*,err=111,end=111) (gthet(j,i),j=1,3)
read (ithep_pdb,*,err=111,end=111) theta0(i),sig0(i),sigc0(i)
sigc0(i)=sigc0(i)**2
enddo
+ do i=1,ntyp
+ athet(1,i,1,-1)=athet(1,i,1,1)
+ athet(2,i,1,-1)=athet(2,i,1,1)
+ bthet(1,i,1,-1)=-bthet(1,i,1,1)
+ bthet(2,i,1,-1)=-bthet(2,i,1,1)
+ athet(1,i,-1,1)=-athet(1,i,1,1)
+ athet(2,i,-1,1)=-athet(2,i,1,1)
+ bthet(1,i,-1,1)=bthet(1,i,1,1)
+ bthet(2,i,-1,1)=bthet(2,i,1,1)
+ enddo
+ do i=-ntyp,-1
+ a0thet(i)=a0thet(-i)
+ athet(1,i,-1,-1)=athet(1,-i,1,1)
+ athet(2,i,-1,-1)=-athet(2,-i,1,1)
+ bthet(1,i,-1,-1)=bthet(1,-i,1,1)
+ bthet(2,i,-1,-1)=-bthet(2,-i,1,1)
+ athet(1,i,-1,1)=athet(1,-i,1,1)
+ athet(2,i,-1,1)=-athet(2,-i,1,1)
+ bthet(1,i,-1,1)=-bthet(1,-i,1,1)
+ bthet(2,i,-1,1)=bthet(2,-i,1,1)
+ athet(1,i,1,-1)=-athet(1,-i,1,1)
+ athet(2,i,1,-1)=athet(2,-i,1,1)
+ bthet(1,i,1,-1)=bthet(1,-i,1,1)
+ bthet(2,i,1,-1)=-bthet(2,-i,1,1)
+ theta0(i)=theta0(-i)
+ sig0(i)=sig0(-i)
+ sigc0(i)=sigc0(-i)
+ do j=0,3
+ polthet(j,i)=polthet(j,-i)
+ enddo
+ do j=1,3
+ gthet(j,i)=gthet(j,-i)
+ enddo
+ enddo
write (2,*) "End reading THETA_PDB"
close (ithep_pdb)
#endif
bsc(1,i)=0.0D0
read(irotam,*,end=112,err=112)(censc(k,1,i),k=1,3),
& ((blower(k,l,1),l=1,k),k=1,3)
- censc(1,1,-i)=censc(1,1,i)
- censc(2,1,-i)=censc(2,1,i)
- censc(3,1,-i)=-censc(3,1,i)
-
do j=2,nlob(i)
read (irotam,*,end=112,err=112) bsc(j,i)
read (irotam,*,end=112,err=112) (censc(k,j,i),k=1,3),
& ((blower(k,l,j),l=1,k),k=1,3)
- censc(1,j,-i)=censc(1,j,i)
- censc(2,j,-i)=censc(2,j,i)
- censc(3,j,-i)=-censc(3,j,i)
- C BSC is amplitude of Gaussian
enddo
do j=1,nlob(i)
do k=1,3
enddo
gaussc(k,l,j,i)=akl
gaussc(l,k,j,i)=akl
- if (((k.eq.3).and.(l.ne.3))
- & .or.((l.eq.3).and.(k.ne.3))) then
- gaussc(k,l,j,-i)=-akl
- gaussc(l,k,j,-i)=-akl
- else
- gaussc(k,l,j,-i)=akl
- gaussc(l,k,j,-i)=akl
- endif
enddo
enddo
enddo
C Read the parameters of the probability distribution/energy expression
C of the side chains.
C
+ write (2,*) "Start reading ROTAM_PDB"
+
do i=1,ntyp
read (irotam_pdb,'(3x,i3,f8.3)',end=112,err=112) nlob(i),dsc(i)
if (i.eq.10) then
endif
enddo
close (irotam_pdb)
+ write (2,*) "Ending reading ROTAM_PDB"
#endif
close(irotam)
C
read (itorp,*,end=113,err=113) ntortyp
read (itorp,*,end=113,err=113) (itortyp(i),i=1,ntyp)
- do iblock=1,2
- do i=-ntyp,-1
- itortyp(i)=-itortyp(-i)
- enddo
c write (iout,*) 'ntortyp',ntortyp
- do i=0,ntortyp-1
- do j=-ntortyp+1,ntortyp-1
- read (itorp,*,end=113,err=113) nterm(i,j,iblock),
- & nlor(i,j,iblock)
- nterm(-i,-j,iblock)=nterm(i,j,iblock)
- nlor(-i,-j,iblock)=nlor(i,j,iblock)
+ do i=1,ntortyp
+ do j=1,ntortyp
+ read (itorp,*,end=113,err=113) nterm(i,j),nlor(i,j)
v0ij=0.0d0
si=-1.0d0
- do k=1,nterm(i,j,iblock)
- read (itorp,*,end=113,err=113) kk,v1(k,i,j,iblock),
- & v2(k,i,j,iblock)
- v1(k,-i,-j,iblock)=v1(k,i,j,iblock)
- v2(k,-i,-j,iblock)=-v2(k,i,j,iblock)
- v0ij=v0ij+si*v1(k,i,j,iblock)
+ do k=1,nterm(i,j)
+ read (itorp,*,end=113,err=113) kk,v1(k,i,j),v2(k,i,j)
+ v0ij=v0ij+si*v1(k,i,j)
si=-si
- c write(iout,*) i,j,k,iblock,nterm(i,j,iblock)
- c write(iout,*) v1(k,-i,-j,iblock),v1(k,i,j,iblock),
- c &v2(k,-i,-j,iblock),v2(k,i,j,iblock)
enddo
- do k=1,nlor(i,j,iblock)
+ do k=1,nlor(i,j)
read (itorp,*,end=113,err=113) kk,vlor1(k,i,j),
& vlor2(k,i,j),vlor3(k,i,j)
v0ij=v0ij+vlor1(k,i,j)/(1+vlor3(k,i,j)**2)
enddo
- v0(i,j,iblock)=v0ij
- v0(-i,-j,iblock)=v0ij
+ v0(i,j)=v0ij
enddo
enddo
- enddo
close (itorp)
if (lprint) then
write (iout,'(/a/)') 'Torsional constants:'
do j=1,ntortyp
write (iout,*) 'ityp',i,' jtyp',j
write (iout,*) 'Fourier constants'
- do k=1,nterm(i,j,iblock)
- write (iout,'(2(1pe15.5))') v1(k,i,j,iblock),
- & v2(k,i,j,iblock)
+ do k=1,nterm(i,j)
+ write (iout,'(2(1pe15.5))') v1(k,i,j),v2(k,i,j)
enddo
write (iout,*) 'Lorenz constants'
- do k=1,nlor(i,j,iblock)
+ do k=1,nlor(i,j)
write (iout,'(3(1pe15.5))')
& vlor1(k,i,j),vlor2(k,i,j),vlor3(k,i,j)
enddo
C
C 6/23/01 Read parameters for double torsionals
C
- do iblock=1,2
- do i=0,ntortyp-1
- do j=-ntortyp+1,ntortyp-1
- do k=-ntortyp+1,ntortyp-1
+ do i=1,ntortyp
+ do j=1,ntortyp
+ do k=1,ntortyp
read (itordp,'(3a1)',end=114,err=114) t1,t2,t3
++<<<<<<< HEAD
+c write (iout,*) "OK onelett",
+c & i,j,k,t1,t2,t3
+
+ if (t1.ne.toronelet(i) .or. t2.ne.toronelet(j)
+ & .or. t3.ne.toronelet(k)) then
++=======
+ if (t1.ne.onelett(i) .or. t2.ne.onelett(j)
+ & .or. t3.ne.onelett(k)) then
++>>>>>>> devel
write (iout,*) "Error in double torsional parameter file",
& i,j,k,t1,t2,t3
#ifdef MPI
#endif
stop "Error in double torsional parameter file"
endif
- read (itordp,*,end=114,err=114) ntermd_1(i,j,k,iblock),
- & ntermd_2(i,j,k,iblock)
- ntermd_1(-i,-j,-k,iblock)=ntermd_1(i,j,k,iblock)
- ntermd_2(-i,-j,-k,iblock)=ntermd_2(i,j,k,iblock)
- read (itordp,*,end=114,err=114) (v1c(1,l,i,j,k,iblock),l=1,
- & ntermd_1(i,j,k,iblock))
- read (itordp,*,end=114,err=114) (v1s(1,l,i,j,k,iblock),l=1,
- & ntermd_1(i,j,k,iblock))
- read (itordp,*,end=114,err=114) (v1c(2,l,i,j,k,iblock),l=1,
- & ntermd_1(i,j,k,iblock))
- read (itordp,*,end=114,err=114) (v1s(2,l,i,j,k,iblock),l=1,
- & ntermd_1(i,j,k,iblock))
- C Martix of D parameters for one dimesional foureir series
- do l=1,ntermd_1(i,j,k,iblock)
- v1c(1,l,-i,-j,-k,iblock)=v1c(1,l,i,j,k,iblock)
- v1s(1,l,-i,-j,-k,iblock)=-v1s(1,l,i,j,k,iblock)
- v1c(2,l,-i,-j,-k,iblock)=v1c(2,l,i,j,k,iblock)
- v1s(2,l,-i,-j,-k,iblock)=-v1s(2,l,i,j,k,iblock)
- c write(iout,*) "whcodze" ,
- c & v1s(2,l,-i,-j,-k,iblock),v1s(2,l,i,j,k,iblock)
- enddo
- read (itordp,*,end=114,err=114) ((v2c(l,m,i,j,k,iblock),
- & v2c(m,l,i,j,k,iblock),v2s(l,m,i,j,k,iblock),
- & v2s(m,l,i,j,k,iblock),
- & m=1,l-1),l=1,ntermd_2(i,j,k,iblock))
- C Martix of D parameters for two dimesional fourier series
- do l=1,ntermd_2(i,j,k,iblock)
- do m=1,l-1
- v2c(l,m,-i,-j,-k,iblock)=v2c(l,m,i,j,k,iblock)
- v2c(m,l,-i,-j,-k,iblock)=v2c(m,l,i,j,k,iblock)
- v2s(l,m,-i,-j,-k,iblock)=-v2s(l,m,i,j,k,iblock)
- v2s(m,l,-i,-j,-k,iblock)=-v2s(m,l,i,j,k,iblock)
- enddo!m
- enddo!l
- enddo!k
- enddo!j
- enddo!i
- enddo!iblock
+ read (itordp,*,end=114,err=114) ntermd_1(i,j,k),
+ & ntermd_2(i,j,k)
+ read (itordp,*,end=114,err=114) (v1c(1,l,i,j,k),l=1,
+ & ntermd_1(i,j,k))
+ read (itordp,*,end=114,err=114) (v1s(1,l,i,j,k),l=1,
+ & ntermd_1(i,j,k))
+ read (itordp,*,end=114,err=114) (v1c(2,l,i,j,k),l=1,
+ & ntermd_1(i,j,k))
+ read (itordp,*,end=114,err=114) (v1s(2,l,i,j,k),l=1,
+ & ntermd_1(i,j,k))
+ read (itordp,*,end=114,err=114) ((v2c(l,m,i,j,k),
+ & v2c(m,l,i,j,k),v2s(l,m,i,j,k),v2s(m,l,i,j,k),
+ & m=1,l-1),l=1,ntermd_2(i,j,k))
+ enddo
+ enddo
+ enddo
if (lprint) then
write (iout,*)
write (iout,*) 'Constants for double torsionals'
++<<<<<<< HEAD
+ do iblock=1,2
+ do i=0,ntortyp-1
+ do j=-ntortyp+1,ntortyp-1
+ do k=-ntortyp+1,ntortyp-1
++=======
+ do i=1,ntortyp
+ do j=1,ntortyp
+ do k=1,ntortyp
++>>>>>>> devel
write (iout,*) 'ityp',i,' jtyp',j,' ktyp',k,
- & ' nsingle',ntermd_1(i,j,k,iblock),
- & ' ndouble',ntermd_2(i,j,k,iblock)
+ & ' nsingle',ntermd_1(i,j,k),' ndouble',ntermd_2(i,j,k)
write (iout,*)
write (iout,*) 'Single angles:'
- do l=1,ntermd_1(i,j,k,iblock)
- write (iout,'(i5,2f10.5,5x,2f10.5,5x,2f10.5)') l,
- & v1c(1,l,i,j,k,iblock),v1s(1,l,i,j,k,iblock),
- & v1c(2,l,i,j,k,iblock),v1s(2,l,i,j,k,iblock),
- & v1s(1,l,-i,-j,-k,iblock),v1s(2,l,-i,-j,-k,iblock)
+ do l=1,ntermd_1(i,j,k)
+ write (iout,'(i5,2f10.5,5x,2f10.5)') l,
+ & v1c(1,l,i,j,k),v1s(1,l,i,j,k),
+ & v1c(2,l,i,j,k),v1s(2,l,i,j,k)
enddo
write (iout,*)
write (iout,*) 'Pairs of angles:'
- write (iout,'(3x,20i10)') (l,l=1,ntermd_2(i,j,k,iblock))
- do l=1,ntermd_2(i,j,k,iblock)
+ write (iout,'(3x,20i10)') (l,l=1,ntermd_2(i,j,k))
+ do l=1,ntermd_2(i,j,k)
write (iout,'(i5,20f10.5)')
- & l,(v2c(l,m,i,j,k,iblock),m=1,ntermd_2(i,j,k,iblock))
+ & l,(v2c(l,m,i,j,k),m=1,ntermd_2(i,j,k))
enddo
write (iout,*)
- write (iout,'(3x,20i10)') (l,l=1,ntermd_2(i,j,k,iblock))
- do l=1,ntermd_2(i,j,k,iblock)
+ write (iout,'(3x,20i10)') (l,l=1,ntermd_2(i,j,k))
+ do l=1,ntermd_2(i,j,k)
write (iout,'(i5,20f10.5)')
- & l,(v2s(l,m,i,j,k,iblock),m=1,ntermd_2(i,j,k,iblock)),
- & (v2s(l,m,-i,-j,-k,iblock),m=1,ntermd_2(i,j,k,iblock))
+ & l,(v2s(l,m,i,j,k),m=1,ntermd_2(i,j,k))
enddo
write (iout,*)
enddo
enddo
enddo
- enddo
endif
#endif
C Read of Side-chain backbone correlation parameters
C Modified 11 May 2012 by Adasko
CCC
C
++<<<<<<< HEAD
+ read (isccor,*,end=119,err=119) nsccortyp
+#ifdef SCCORPDB
+ read (isccor,*,end=119,err=119) (isccortyp(i),i=1,ntyp)
+ do i=-ntyp,-1
+ isccortyp(i)=-isccortyp(-i)
+ enddo
+ iscprol=isccortyp(20)
++=======
+ read (isccor,*,end=1113,err=1113) nsccortyp
+ read (isccor,*,end=1113,err=1113) (isccortyp(i),i=1,ntyp)
++>>>>>>> devel
c write (iout,*) 'ntortyp',ntortyp
maxinter=3
cc maxinter is maximum interaction sites
do l=1,maxinter
do i=1,nsccortyp
do j=1,nsccortyp
++<<<<<<< HEAD
+ read (isccor,*,end=119,err=119) nterm_sccor(i,j),nlor_sccor(i,j)
++=======
+ read (isccor,*,end=1113,err=1113) nterm_sccor(i,j),
+ & nlor_sccor(i,j)
++>>>>>>> devel
v0ijsccor=0.0d0
+ v0ijsccor1=0.0d0
+ v0ijsccor2=0.0d0
+ v0ijsccor3=0.0d0
si=-1.0d0
-
+ nterm_sccor(-i,j)=nterm_sccor(i,j)
+ nterm_sccor(-i,-j)=nterm_sccor(i,j)
+ nterm_sccor(i,-j)=nterm_sccor(i,j)
do k=1,nterm_sccor(i,j)
++<<<<<<< HEAD
+ read (isccor,*,end=119,err=119) kk,v1sccor(k,l,i,j)
+ & ,v2sccor(k,l,i,j)
+ if (j.eq.iscprol) then
+ if (i.eq.isccortyp(10)) then
+ v1sccor(k,l,i,-j)=v1sccor(k,l,i,j)
+ v2sccor(k,l,i,-j)=-v2sccor(k,l,i,j)
+ else
+ v1sccor(k,l,i,-j)=v1sccor(k,l,i,j)*0.5d0
+ & +v2sccor(k,l,i,j)*dsqrt(0.75d0)
+ v2sccor(k,l,i,-j)=-v2sccor(k,l,i,j)*0.5d0
+ & +v1sccor(k,l,i,j)*dsqrt(0.75d0)
+ v1sccor(k,l,-i,-j)=v1sccor(k,l,i,j)
+ v2sccor(k,l,-i,-j)=-v2sccor(k,l,i,j)
+ v1sccor(k,l,-i,j)=v1sccor(k,l,i,-j)
+ v2sccor(k,l,-i,j)=-v2sccor(k,l,i,-j)
+ endif
+ else
+ if (i.eq.isccortyp(10)) then
+ v1sccor(k,l,i,-j)=v1sccor(k,l,i,j)
+ v2sccor(k,l,i,-j)=-v2sccor(k,l,i,j)
+ else
+ if (j.eq.isccortyp(10)) then
+ v1sccor(k,l,-i,j)=v1sccor(k,l,i,j)
+ v2sccor(k,l,-i,j)=-v2sccor(k,l,i,j)
+ else
+ v1sccor(k,l,i,-j)=-v1sccor(k,l,i,j)
+ v2sccor(k,l,i,-j)=-v2sccor(k,l,i,j)
+ v1sccor(k,l,-i,-j)=v1sccor(k,l,i,j)
+ v2sccor(k,l,-i,-j)=-v2sccor(k,l,i,j)
+ v1sccor(k,l,-i,j)=v1sccor(k,l,i,-j)
+ v2sccor(k,l,-i,j)=-v2sccor(k,l,i,-j)
+ endif
+ endif
+ endif
++=======
+ read (isccor,*,end=1113,err=1113) kk,v1sccor(k,l,i,j)
+ & ,v2sccor(k,l,i,j)
++>>>>>>> devel
v0ijsccor=v0ijsccor+si*v1sccor(k,l,i,j)
+ v0ijsccor1=v0ijsccor+si*v1sccor(k,l,-i,j)
+ v0ijsccor2=v0ijsccor+si*v1sccor(k,l,i,-j)
+ v0ijsccor3=v0ijsccor+si*v1sccor(k,l,-i,-j)
si=-si
enddo
do k=1,nlor_sccor(i,j)
++<<<<<<< HEAD
+ read (isccor,*,end=119,err=119) kk,vlor1sccor(k,i,j),
++=======
+ read (isccor,*,end=1113,err=1113) kk,vlor1sccor(k,i,j),
++>>>>>>> devel
& vlor2sccor(k,i,j),vlor3sccor(k,i,j)
v0ijsccor=v0ijsccor+vlor1sccor(k,i,j)/
&(1+vlor3sccor(k,i,j)**2)
enddo
- v0sccor(i,j)=v0ijsccor
+ v0sccor(l,i,j)=v0ijsccor
+ v0sccor(l,-i,j)=v0ijsccor1
+ v0sccor(l,i,-j)=v0ijsccor2
+ v0sccor(l,-i,-j)=v0ijsccor3
enddo
enddo
enddo
close (isccor)
-
+#else
+ read (isccor,*,end=119,err=119) (isccortyp(i),i=1,ntyp)
+c write (iout,*) 'ntortyp',ntortyp
+ maxinter=3
+cc maxinter is maximum interaction sites
+ do l=1,maxinter
+ do i=1,nsccortyp
+ do j=1,nsccortyp
+ read (isccor,*,end=119,err=119)
+ & nterm_sccor(i,j),nlor_sccor(i,j)
+ v0ijsccor=0.0d0
+ si=-1.0d0
+
+ do k=1,nterm_sccor(i,j)
+ read (isccor,*,end=119,err=119) kk,v1sccor(k,l,i,j)
+ & ,v2sccor(k,l,i,j)
+ v0ijsccor=v0ijsccor+si*v1sccor(k,l,i,j)
+ si=-si
+ enddo
+ do k=1,nlor_sccor(i,j)
+ read (isccor,*,end=119,err=119) kk,vlor1sccor(k,i,j),
+ & vlor2sccor(k,i,j),vlor3sccor(k,i,j)
+ v0ijsccor=v0ijsccor+vlor1sccor(k,i,j)/
+ &(1+vlor3sccor(k,i,j)**2)
+ enddo
+ v0sccor(i,j,iblock)=v0ijsccor
+ enddo
+ enddo
+ enddo
+ close (isccor)
+
+#endif
if (lprint) then
write (iout,'(/a/)') 'Torsional constants:'
do i=1,nsccortyp
write (iout,*) "Coefficients of the cumulants"
endif
read (ifourier,*) nloctyp
- do i=0,nloctyp-1
+ do i=1,nloctyp
read (ifourier,*,end=115,err=115)
read (ifourier,*,end=115,err=115) (b(ii),ii=1,13)
if (lprint) then
endif
B1(1,i) = b(3)
B1(2,i) = b(5)
c b1(1,i)=0.0d0
c b1(2,i)=0.0d0
B1tilde(1,i) = b(3)
++<<<<<<< HEAD
+ B1tilde(2,i) =-b(5)
+ B1tilde(1,-i) =-b(3)
+ B1tilde(2,-i) =b(5)
++=======
+ B1tilde(2,i) =-b(5)
++>>>>>>> devel
c b1tilde(1,i)=0.0d0
c b1tilde(2,i)=0.0d0
B2(1,i) = b(2)
B2(2,i) = b(4)
- B2(1,-i) =b(2)
- B2(2,-i) =-b(4)
-
c b2(1,i)=0.0d0
c b2(2,i)=0.0d0
CC(1,1,i)= b(7)
CC(2,2,i)=-b(7)
CC(2,1,i)= b(9)
CC(1,2,i)= b(9)
- CC(1,1,-i)= b(7)
- CC(2,2,-i)=-b(7)
- CC(2,1,-i)=-b(9)
- CC(1,2,-i)=-b(9)
c CC(1,1,i)=0.0d0
c CC(2,2,i)=0.0d0
c CC(2,1,i)=0.0d0
Ctilde(1,2,i)=b(9)
Ctilde(2,1,i)=-b(9)
Ctilde(2,2,i)=b(7)
- Ctilde(1,1,-i)=b(7)
- Ctilde(1,2,-i)=-b(9)
- Ctilde(2,1,-i)=b(9)
- Ctilde(2,2,-i)=b(7)
-
c Ctilde(1,1,i)=0.0d0
c Ctilde(1,2,i)=0.0d0
c Ctilde(2,1,i)=0.0d0
DD(2,2,i)=-b(6)
DD(2,1,i)= b(8)
DD(1,2,i)= b(8)
- DD(1,1,-i)= b(6)
- DD(2,2,-i)=-b(6)
- DD(2,1,-i)=-b(8)
- DD(1,2,-i)=-b(8)
c DD(1,1,i)=0.0d0
c DD(2,2,i)=0.0d0
c DD(2,1,i)=0.0d0
Dtilde(1,2,i)=b(8)
Dtilde(2,1,i)=-b(8)
Dtilde(2,2,i)=b(6)
- Dtilde(1,1,-i)=b(6)
- Dtilde(1,2,-i)=-b(8)
- Dtilde(2,1,-i)=b(8)
- Dtilde(2,2,-i)=b(6)
-
c Dtilde(1,1,i)=0.0d0
c Dtilde(1,2,i)=0.0d0
c Dtilde(2,1,i)=0.0d0
EE(2,2,i)=-b(10)+b(11)
EE(2,1,i)= b(12)-b(13)
EE(1,2,i)= b(12)+b(13)
- EE(1,1,-i)= b(10)+b(11)
- EE(2,2,-i)=-b(10)+b(11)
- EE(2,1,-i)=-b(12)+b(13)
- EE(1,2,-i)=-b(12)-b(13)
-
c ee(1,1,i)=1.0d0
c ee(2,2,i)=1.0d0
c ee(2,1,i)=0.0d0
endif
goto 50
C---------------------- GB or BP potential -----------------------------
- 30 read (isidep,*,end=116,err=116)((eps(i,j),j=i,ntyp),i=1,ntyp),
- & (sigma0(i),i=1,ntyp),(sigii(i),i=1,ntyp),(chip(i),i=1,ntyp),
- & (alp(i),i=1,ntyp)
+ 30 do i=1,ntyp
+ read (isidep,*,end=116,err=116)(eps(i,j),j=i,ntyp)
+ enddo
+ read (isidep,*,end=116,err=116)(sigma0(i),i=1,ntyp)
+ read (isidep,*,end=116,err=116)(sigii(i),i=1,ntyp)
+ read (isidep,*,end=116,err=116)(chip(i),i=1,ntyp)
+ read (isidep,*,end=116,err=116)(alp(i),i=1,ntyp)
+
+c 30 read (isidep,*,end=116,err=116)((eps(i,j),j=i,ntyp),i=1,ntyp),
+c & (sigma0(i),i=1,ntyp),(sigii(i),i=1,ntyp),(chip(i),i=1,ntyp),
+c & (alp(i),i=1,ntyp)
C For the GB potential convert sigma'**2 into chi'
if (ipot.eq.4) then
do i=1,ntyp
C
C Define the SC-p interaction constants (hard-coded; old style)
C
- do i=1,20
+ do i=1,ntyp
C "Soft" SC-p repulsion (causes helices to be too flat, but facilitates
C helix formation)
c aad(i,1)=0.3D0*4.0D0**12
if (lprint) then
write (iout,*) "Parameters of SC-p interactions:"
- do i=1,20
+ do i=1,ntyp
write (iout,'(4f8.3,4e12.4)') eps_scp(i,1),rscp(i,1),
& eps_scp(i,2),rscp(i,2),aad(i,1),bad(i,1),aad(i,2),bad(i,2)
enddo
goto 999
113 write (iout,*) "Error reading torsional energy parameters."
goto 999
+ 1113 write (iout,*)
+ & "Error reading side-chain torsional energy parameters."
+ goto 999
114 write (iout,*) "Error reading double torsional energy parameters."
goto 999
115 write (iout,*)
character*3 seq,atom,res
character*80 card
dimension sccor(3,20)
+ double precision e1(3),e2(3),e3(3)
+ logical fail
integer rescode
ibeg=1
lsecondary=.false.
ishift=ires-1
if (res.ne.'GLY' .and. res.ne. 'ACE') then
ishift=ishift-1
- itype(1)=21
+ itype(1)=ntyp1
endif
ibeg=0
endif
nstart_sup=1
if (itype(nres).ne.10) then
nres=nres+1
- itype(nres)=21
+ itype(nres)=ntyp1
if (unres_pdb) then
- c(1,nres)=c(1,nres-1)+3.8d0
- c(2,nres)=c(2,nres-1)
- c(3,nres)=c(3,nres-1)
+ C 2/15/2013 by Adam: corrected insertion of the last dummy residue
+ call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
+ if (fail) then
+ e2(1)=0.0d0
+ e2(2)=1.0d0
+ e2(3)=0.0d0
+ endif
+ do j=1,3
+ c(j,nres)=c(j,nres-1)-3.8d0*e2(j)
+ enddo
else
do j=1,3
dcj=c(j,nres-2)-c(j,nres-3)
c(j,nres+1)=c(j,1)
c(j,2*nres)=c(j,nres)
enddo
- if (itype(1).eq.21) then
+ if (itype(1).eq.ntyp1) then
nsup=nsup-1
nstart_sup=2
if (unres_pdb) then
- c(1,1)=c(1,2)-3.8d0
- c(2,1)=c(2,2)
- c(3,1)=c(3,2)
+ C 2/15/2013 by Adam: corrected insertion of the first dummy residue
+ call refsys(2,3,4,e1,e2,e3,fail)
+ if (fail) then
+ e2(1)=0.0d0
+ e2(2)=1.0d0
+ e2(3)=0.0d0
+ endif
+ do j=1,3
+ c(j,1)=c(j,2)-3.8d0*e2(j)
+ enddo
else
do j=1,3
dcj=c(j,4)-c(j,3)
enddo
iti=itype(i)
di=dist(i,nres+i)
+ C 10/03/12 Adam: Correction for zero SC-SC bond length
+ if (itype(i).ne.10 .and. itype(i).ne.21. and. di.eq.0.0d0)
+ & di=dsc(itype(i))
vbld(i+nres)=di
if (itype(i).ne.10) then
vbld_inv(i+nres)=1.0d0/di
enddo
return
end
-
call reada(weightcard,"V2SS",v2ss,7.61d0)
call reada(weightcard,"V3SS",v3ss,13.7d0)
call reada(weightcard,"EBR",ebr,-5.50D0)
+ dyn_ss=(index(weightcard,'DYN_SS').gt.0)
+ do i=1,maxres
+ dyn_ss_mask(i)=.false.
+ enddo
+ do i=1,maxres-1
+ do j=i+1,maxres
+ dyn_ssbond_ij(i,j)=1.0d300
+ enddo
+ enddo
+ call reada(weightcard,"HT",Ht,0.0D0)
+ if (dyn_ss) then
+ ss_depth=ebr/wsc-0.25*eps(1,1)
+ Ht=Ht/wsc-0.25*eps(1,1)
+ akcm=akcm*wstrain/wsc
+ akth=akth*wstrain/wsc
+ akct=akct*wstrain/wsc
+ v1ss=v1ss*wstrain/wsc
+ v2ss=v2ss*wstrain/wsc
+ v3ss=v3ss*wstrain/wsc
+ else
+ ss_depth=ebr/wstrain-0.25*eps(1,1)*wsc/wstrain
+ endif
+
if(me.eq.king.or..not.out1file) then
write (iout,*) "Parameters of the SS-bond potential:"
write (iout,*) "D0CM",d0cm," AKCM",akcm," AKTH",akth,
& " AKCT",akct
write (iout,*) "V1SS",v1ss," V2SS",v2ss," V3SS",v3ss
- write (iout,*) "EBR",ebr
+ write (iout,*) "EBR",ebr," SS_DEPTH",ss_depth
+ write (iout,*)" HT",Ht
print *,'indpdb=',indpdb,' pdbref=',pdbref
endif
if (indpdb.gt.0 .or. pdbref) then
call contact(.false.,ncont_ref,icont_ref,co)
if (sideadd) then
+ C Following 2 lines for diagnostics; comment out if not needed
+ write (iout,*) "Before sideadd"
+ call intout
if(me.eq.king.or..not.out1file)
& write(iout,*)'Adding sidechains'
maxsi=1000
& i,' after ',nsi,' trials'
endif
enddo
+ C 10/03/12 Adam: Recalculate coordinates with new side chain positions
+ call chainbuild
endif
+ C Following 2 lines for diagnostics; comment out if not needed
+ c write (iout,*) "After sideadd"
+ c call intout
endif
if (indpdb.eq.0) then
C Read sequence if not taken from the pdb file.
vbld_inv(i)=vblinv
enddo
do i=2,nres-1
- vbld(i+nres)=dsc(iabs(itype(i)))
- vbld_inv(i+nres)=dsc_inv(iabs(itype(i)))
+ vbld(i+nres)=dsc(itype(i))
+ vbld_inv(i+nres)=dsc_inv(itype(i))
c write (iout,*) "i",i," itype",itype(i),
c & " dsc",dsc(itype(i))," vbld",vbld(i),vbld(i+nres)
enddo
c print '(20i4)',(itype(i),i=1,nres)
do i=1,nres
#ifdef PROCOR
- if (itype(i).eq.21 .or. itype(i+1).eq.21) then
+ if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) then
#else
- if (itype(i).eq.21) then
+ if (itype(i).eq.ntyp1) then
#endif
itel(i)=0
#ifdef PROCOR
- else if (iabs(itype(i+1)).ne.20) then
+ else if (itype(i+1).ne.20) then
#else
- else if (iabs(itype(i)).ne.20) then
+ else if (itype(i).ne.20) then
#endif
itel(i)=1
else
#endif
nct=nres
cd print *,'NNT=',NNT,' NCT=',NCT
- if (itype(1).eq.21) nnt=2
- if (itype(nres).eq.21) nct=nct-1
+ if (itype(1).eq.ntyp1) nnt=2
+ if (itype(nres).eq.ntyp1) nct=nct-1
if (pdbref) then
if(me.eq.king.or..not.out1file)
& write (iout,'(a,i3)') 'nsup=',nsup
c write (iout,*) "constr_dist",constr_dist,nstart_sup,nsup
if (constr_dist.gt.0) then
call read_dist_constr
- call hpb_partition
endif
+ if (nhpb.gt.0) call hpb_partition
c write (iout,*) "After read_dist_constr nhpb",nhpb
c call flush(iout)
if (indpdb.eq.0 .and. modecalc.ne.2 .and. modecalc.ne.4
enddo
do i=2,nres-1
omeg(i)=-120d0*deg2rad
- if (itype(i).le.0) omeg(i)=-omeg(i)
enddo
else
if(me.eq.king.or..not.out1file)
write (iout,'(/a,i3,a)')
& 'The chain contains',ns,' disulfide-bridging cysteines.'
write (iout,'(20i4)') (iss(i),i=1,ns)
+ if (dyn_ss) then
+ write(iout,*)"Running with dynamic disulfide-bond formation"
+ else
write (iout,'(/a/)') 'Pre-formed links are:'
do i=1,nss
i1=ihpb(i)-nres
i2=jhpb(i)-nres
it1=itype(i1)
it2=itype(i2)
- if (me.eq.king.or..not.out1file)
- & write (iout,'(2a,i3,3a,i3,a,3f10.3)')
+ write (iout,'(2a,i3,3a,i3,a,3f10.3)')
& restyp(it1),'(',i1,') -- ',restyp(it2),'(',i2,')',dhpb(i),
& ebr,forcon(i)
enddo
write (iout,'(a)')
+ endif
+ endif
+ if (ns.gt.0.and.dyn_ss) then
+ do i=nss+1,nhpb
+ ihpb(i-nss)=ihpb(i)
+ jhpb(i-nss)=jhpb(i)
+ forcon(i-nss)=forcon(i)
+ dhpb(i-nss)=dhpb(i)
+ enddo
+ nhpb=nhpb-nss
+ nss=0
+ call hpb_partition
+ do i=1,ns
+ dyn_ss_mask(iss(i))=.true.
+ enddo
endif
if (i2ndstr.gt.0) call secstrp2dihc
c call geom_to_var(nvar,x)
do i=1,ns
if (itype(iss(i)).ne.1) then
if (me.eq.king.or..not.out1file) write (iout,'(2a,i3,a)')
- & 'Do you REALLY think that the residue ',restyp(iss(i)),i,
+ & 'Do you REALLY think that the residue ',
+ & restyp(itype(iss(i))),i,
& ' can form a disulfide bridge?!!!'
write (*,'(2a,i3,a)')
- & 'Do you REALLY think that the residue ',restyp(iss(i)),i,
+ & 'Do you REALLY think that the residue ',
+ & restyp(itype(iss(i))),i,
& ' can form a disulfide bridge?!!!'
#ifdef MPI
call MPI_Finalize(MPI_COMM_WORLD,ierror)
C Read preformed bridges.
if (ns.gt.0) then
read (inp,*) nss,(ihpb(i),jhpb(i),i=1,nss)
- write (iout,*) 'nss=',nss,' ihpb,jhpb: ',(ihpb(i),jhpb(i),i=1,nss)
+ if(fg_rank.eq.0)
+ & write(iout,*)'nss=',nss,' ihpb,jhpb: ',(ihpb(i),jhpb(i),i=1,nss)
if (nss.gt.0) then
nhpb=nss
C Check if the residues involved in bridges are in the specified list of
if (wfrag_(i).gt.0.0d0) then
do j=ifrag_(1,i),ifrag_(2,i)-1
do k=j+1,ifrag_(2,i)
- write (iout,*) "j",j," k",k
+ c write (iout,*) "j",j," k",k
ddjk=dist(j,k)
if (constr_dist.eq.1) then
nhpb=nhpb+1
c Don't do glycine or ends
i=itype(res_pick)
- if (i.eq.10 .or. i.eq.21) return
+ if (i.eq.10 .or. i.eq.ntyp1) return
c Freeze everything (later will relax only selected side-chains)
mask_r=.true.
n_try=0
do while (n_try.lt.n_maxtry .and. orig_e-cur_e.lt.e_drop)
c Move the selected residue (don't worry if it fails)
- call gen_side(iabs(itype(res_pick)),theta(res_pick+1),
+ call gen_side(itype(res_pick),theta(res_pick+1),
+ alph(res_pick),omeg(res_pick),fail)
c Minimize the side-chains starting from the new arrangement
do i=iatsc_s,iatsc_e
- itypi=iabs(itype(i))
- itypi1=iabs(itype(i+1))
+ itypi=itype(i)
+ itypi1=itype(i+1)
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
do j=istart(i,iint),iend(i,iint)
IF (mask_side(j).eq.1.or.mask_side(i).eq.1) THEN
ind=ind+1
- itypj=iabs(itype(j))
+ itypj=itype(j)
dscj_inv=dsc_inv(itypj)
sig0ij=sigma(itypi,itypj)
chi1=chi(itypi,itypj)
do j=1,3
ff(j)=ff(j)+force(j,i)
enddo
- if (itype(i+1).ne.21) then
+ if (itype(i+1).ne.ntyp1) then
do j=1,3
stochforc(j,i)=stochforc(j,i)+force(j,i+nres+1)
ff(j)=ff(j)+force(j,i+nres+1)
ind=ind+1
ii = ind+m
iti=itype(i)
- gamvec(ii)=gamsc(iti)
+ gamvec(ii)=gamsc(iabs(iti))
enddo
if (surfarea) call sdarea(gamvec)
c if (lprn) then
include 'COMMON.INTERACT'
include 'COMMON.IOUNITS'
include 'COMMON.NAMES'
- double precision radius(maxres2),gamvec(maxres6)
+ double precision radius(maxres2),gamvec(maxres2)
parameter (twosix=1.122462048309372981d0)
logical lprn /.false./
c
if (Fortran_COMPILER_NAME STREQUAL "ifort")
set(FFLAGS0 "-g -CB -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres -I${MPIF_INCLUDE_DIRECTORIES}" )
elseif (Fortran_COMPILER_NAME STREQUAL "gfortran")
- set(FFLAGS0 "-g -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres -I${MPIF_INCLUDE_DIRECTORIES}" )
+ set(FFLAGS0 "-std=legacy -g -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres -I${MPIF_INCLUDE_DIRECTORIES}" )
endif (Fortran_COMPILER_NAME STREQUAL "ifort")
set_property(SOURCE ${UNRES_WHAM_M_SRC0} PROPERTY COMPILE_FLAGS ${FFLAGS0} )
#=========================================
- # WHAM preprocesor flags
+ # Settings for GAB force field
#=========================================
+ if(UNRES_MD_FF STREQUAL "GAB" )
+ # set preprocesor flags
+ set(CPPFLAGS "PROCOR -DSPLITELE -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DSCCORPDB" )
++<<<<<<< HEAD
+if(UNRES_MD_FF STREQUAL "GAB" )
+ # set preprocesor flags
+ set(CPPFLAGS "PROCOR -DUNRES -DISNAN -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DSCCORPDB" )
+
++=======
++>>>>>>> devel
#=========================================
# Settings for E0LL2Y force field
#=========================================
elseif(UNRES_MD_FF STREQUAL "E0LL2Y")
# set preprocesor flags
++<<<<<<< HEAD
+ set(CPPFLAGS "PROCOR -DUNRES -DISNAN -DSPLITELE -DLANG0 -DSCCORPDB" )
+endif(UNRES_MD_FF STREQUAL "GAB")
++=======
+ set(CPPFLAGS "PROCOR -DSPLITELE -DSCCORPDB" )
+ endif(UNRES_MD_FF STREQUAL "GAB")
+
+ #=========================================
+ # Additional flags
+ #=========================================
+ set(CPPFLAGS "${CPPFLAGS} -DUNRES -DISNAN")
++>>>>>>> devel
#=========================================
# System specific flags
elseif (Fortran_COMPILER_NAME STREQUAL "gfortran")
# Add old gfortran flags
set(CPPFLAGS "${CPPFLAGS} -DG77")
+ else (Fortran_COMPILER_NAME STREQUAL "ifort")
+ # Default preprocessor flags
+ set(CPPFLAGS "${CPPFLAGS} -DPGI")
endif (Fortran_COMPILER_NAME STREQUAL "ifort")
#=========================================
set(UNRES_WHAM_M_BIN "wham_${Fortran_COMPILER_NAME}.exe")
#=========================================
- # cinfo.f stupid workaround for cmake
- # - shame on me ]:)
+ # cinfo.f workaround for CMake
#=========================================
- set_property(SOURCE compinfo.c PROPERTY CMAKE_C_FLAGS "-c" )
- add_executable(compinfo-wham-m compinfo.c)
- set_target_properties(compinfo-wham-m PROPERTIES OUTPUT_NAME compinfo)
+ # get the current date
+ TODAY(DATE)
+ # generate cinfo.f
+
+ set(CINFO "${CMAKE_CURRENT_BINARY_DIR}/cinfo.f")
+ FILE(WRITE ${CINFO}
+ "C CMake generated file
+ subroutine cinfo
+ include 'COMMON.IOUNITS'
+ write(iout,*)'++++ Compile info ++++'
+ write(iout,*)'Version ${UNRES_MAJOR}.${UNRES_MINOR} build ${UNRES_PATCH}'
+ ")
+
+ CINFO_FORMAT(${CINFO} "Compiled" "${DATE}" )
+ CINFO_FORMAT(${CINFO} "Compiled by" "$ENV{USER}@$ENV{HOST}" )
+ CINFO_FORMAT(${CINFO} "OS name:" "${CMAKE_SYSTEM_NAME}" )
+ CINFO_FORMAT(${CINFO} "OS release:" "${CMAKE_SYSTEM}" )
+ CINFO_FORMAT(${CINFO} "Fortran Compiler:" "${CMAKE_Fortran_COMPILER}" )
+ CINFO_FORMAT(${CINFO} "MD Force field:" "${UNRES_MD_FF}" )
+ CINFO_FORMAT(${CINFO} "CPPFLAGS =" "${CPPFLAGS}")
+
+ FILE(APPEND ${CINFO}
+ " write(iout,*)'++++ End of compile info ++++'
+ return
+ end ")
- set(UNRES_CINFO_DIR "${CMAKE_CURRENT_BINARY_DIR}" )
- add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/cinfo.f
- COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/cinfo.f ${CMAKE_CURRENT_BINARY_DIR}/cinfo.f
- COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/COMMON.IOUNITS ${CMAKE_CURRENT_BINARY_DIR}/COMMON.IOUNITS
- COMMAND ${CMAKE_CURRENT_BINARY_DIR}/compinfo | true
- DEPENDS compinfo-wham-m )
- set_property(SOURCE ${UNRES_CINFO_DIR}/cinfo.f PROPERTY COMPILE_FLAGS ${FFLAGS0} )
+ # set include paths
+ set_property(SOURCE ${CMAKE_CURRENT_BINARY_DIR}/cinfo.f PROPERTY COMPILE_FLAGS "${FFLAGS0} -I${CMAKE_CURRENT_SOURCE_DIR}" )
#=========================================
# Set full unres CSA sources
#=========================================
- set(UNRES_WHAM_M_SRCS ${UNRES_WHAM_M_SRC0} ${UNRES_CINFO_DIR}/cinfo.f proc_proc.c)
+ set(UNRES_WHAM_M_SRCS ${UNRES_WHAM_M_SRC0} ${CMAKE_CURRENT_BINARY_DIR}/cinfo.f proc_proc.c)
#=========================================
# Build the binary
& +wturn3*fact(2)*gel_loc_turn3(i)
& +wturn6*fact(5)*gel_loc_turn6(i)
& +wel_loc*fact(2)*gel_loc_loc(i)
- & +wsccor*fact(1)*gsccor_loc(i)
enddo
endif
return
evdw=0.0D0
evdw_t=0.0d0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
cd write (iout,*) 'i=',i,' iint=',iint,' istart=',istart(i,iint),
cd & 'iend=',iend(i,iint)
do j=istart(i,iint),iend(i,iint)
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
zj=c(3,nres+j)-zi
evdw=0.0D0
evdw_t=0.0d0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
C
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
zj=c(3,nres+j)-zi
c endif
ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
ind=ind+1
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
dscj_inv=vbld_inv(j+nres)
chi1=chi(itypi,itypj)
chi2=chi(itypj,itypi)
c if (icall.gt.0) lprn=.true.
ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
ind=ind+1
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
dscj_inv=vbld_inv(j+nres)
sig0ij=sigma(itypi,itypj)
chi1=chi(itypi,itypj)
c if (icall.gt.0) lprn=.true.
ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
ind=ind+1
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
dscj_inv=vbld_inv(j+nres)
sig0ij=sigma(itypi,itypj)
r0ij=r0(itypi,itypj)
gcorr_loc(i)=0.0d0
enddo
do i=iatel_s,iatel_e
- if (itype(i).eq.21 .or. itype(i+1).eq.21) cycle
+ if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
if (itel(i).eq.0) goto 1215
dxi=dc(1,i)
dyi=dc(2,i)
num_conti=0
c write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
do j=ielstart(i),ielend(i)
- if (itype(j).eq.21 .or. itype(j+1).eq.21) cycle
+ if (itype(j).eq.ntyp1 .or. itype(j+1).eq.ntyp1) cycle
if (itel(j).eq.0) goto 1216
ind=ind+1
iteli=itel(i)
ees0ij=4.0D0+fac*fac-3.0D0*(cosb*cosb+cosg*cosg)
ees=ees+eesij
evdw1=evdw1+evdwij
-cd write(iout,'(2(2i3,2x),7(1pd12.4)/2(3(1pd12.4),5x)/)')
-cd & iteli,i,itelj,j,aaa,bbb,ael6i,ael3i,
-cd & 1.0D0/dsqrt(rrmij),evdwij,eesij,
-cd & xmedi,ymedi,zmedi,xj,yj,zj
+c write (iout,'(a6,2i5,0pf7.3,2i5,2e11.3)')
+c &'evdw1',i,j,evdwij
+c &,iteli,itelj,aaa,evdw1
+
+c write (iout,'(a6,2i5,0pf7.3)') 'ees',i,j,eesij
+c write(iout,'(2(2i3,2x),7(1pd12.4)/2(3(1pd12.4),5x)/)')
+c & iteli,i,itelj,j,aaa,bbb,ael6i,ael3i,
+c & 1.0D0/dsqrt(rrmij),evdwij,eesij,
+c & xmedi,ymedi,zmedi,xj,yj,zj
C
C Calculate contributions to the Cartesian gradient.
C
C Contribution to the local-electrostatic energy coming from the i-j pair
eel_loc_ij=a22*muij(1)+a23*muij(2)+a32*muij(3)
& +a33*muij(4)
-cd write (iout,*) 'i',i,' j',j,' eel_loc_ij',eel_loc_ij
-cd write (iout,*) a22,muij(1),a23,muij(2),a32,muij(3)
+c write (iout,*) 'i',i,' j',j,' eel_loc_ij',eel_loc_ij
+c write (iout,'(a6,2i5,0pf7.3)')
+c & 'eelloc',i,j,eel_loc_ij
+c write (iout,*) a22,muij(1),a23,muij(2),a32,muij(3)
eel_loc=eel_loc+eel_loc_ij
C Partial derivatives in virtual-bond dihedral angles gamma
if (calc_grad) then
& +0.5d0*(pizda(1,1)+pizda(2,2))
enddo
endif
- else if (j.eq.i+3 .and. itype(i+2).ne.21) then
+ else if (j.eq.i+3 .and. itype(i+2).ne.ntyp1) then
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
C
C Fourth-order contributions
c write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',iatscp_e,
c & ' scal14',scal14
do i=iatscp_s,iatscp_e
- if (itype(i).eq.21 .or. itype(i+1).eq.21) cycle
+ if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
iteli=itel(i)
c write (iout,*) "i",i," iteli",iteli," nscp_gr",nscp_gr(i),
c & " iscp",(iscpstart(i,j),iscpend(i,j),j=1,nscp_gr(i))
do iint=1,nscp_gr(i)
do j=iscpstart(i,iint),iscpend(i,iint)
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
C Uncomment following three lines for SC-p interactions
c xj=c(1,nres+j)-xi
c yj=c(2,nres+j)-yi
evdw2_14=evdw2_14+e1+e2
endif
evdwij=e1+e2
-c write (iout,*) i,j,evdwij
+c write (iout,'(a6,2i5,0pf7.3,2i3,3e11.3)')
+c & 'evdw2',i,j,evdwij,iteli,itypj,fac,aad(itypj,iteli),
+c & bad(itypj,iteli)
evdw2=evdw2+evdwij
if (calc_grad) then
C
endif
C 24/11/03 AL: SS bridges handled separately because of introducing a specific
C distance and angle dependent SS bond potential.
- if (ii.gt.nres .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then
+ if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and.
+ & iabs(itype(jjj)).eq.1) then
call ssbond_ene(iii,jjj,eij)
ehpb=ehpb+2*eij
else
include 'COMMON.VAR'
include 'COMMON.IOUNITS'
double precision erij(3),dcosom1(3),dcosom2(3),gg(3)
- itypi=itype(i)
+ itypi=iabs(itype(i))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
dyi=dc_norm(2,nres+i)
dzi=dc_norm(3,nres+i)
dsci_inv=dsc_inv(itypi)
- itypj=itype(j)
+ itypj=iabs(itype(j))
dscj_inv=dsc_inv(itypj)
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
logical energy_dec /.false./
double precision u(3),ud(3)
estr=0.0d0
- write (iout,*) "distchainmax",distchainmax
+ estr1=0.0d0
+c write (iout,*) "distchainmax",distchainmax
do i=nnt+1,nct
- if (itype(i-1).eq.21 .or. itype(i).eq.21) then
+ if (itype(i-1).eq.ntyp1 .or. itype(i).eq.ntyp1) then
estr1=estr1+gnmr1(vbld(i),-1.0d0,distchainmax)
do j=1,3
gradb(j,i-1)=gnmr1prim(vbld(i),-1.0d0,distchainmax)
endif
enddo
- estr=0.5d0*AKP*estr
+ estr=0.5d0*AKP*estr+estr1
c
c 09/18/07 AL: multimodal bond potential based on AM1 CA-SC PMF's included
c
do i=nnt,nct
- iti=itype(i)
- if (iti.ne.10 .and. iti.ne.21) then
+ iti=iabs(itype(i))
+ if (iti.ne.10 .and. iti.ne.ntyp1) then
nbi=nbondterm(iti)
if (nbi.eq.1) then
diff=vbld(i+nres)-vbldsc0(1,iti)
c write (*,'(a,i2)') 'EBEND ICG=',icg
c write (iout,*) ithet_start,ithet_end
do i=ithet_start,ithet_end
- if (itype(i-1).eq.21) cycle
+ if (itype(i-1).eq.ntyp1) cycle
C Zero the energy function and its derivative at 0 or pi.
call splinthet(theta(i),0.5d0*delta,ss,ssd)
it=itype(i-1)
- if (i.gt.3 .and. itype(i-2).ne.21) then
+ ichir1=isign(1,itype(i-2))
+ ichir2=isign(1,itype(i))
+ if (itype(i-2).eq.10) ichir1=isign(1,itype(i-1))
+ if (itype(i).eq.10) ichir2=isign(1,itype(i-1))
+ if (itype(i-1).eq.10) then
+ itype1=isign(10,itype(i-2))
+ ichir11=isign(1,itype(i-2))
+ ichir12=isign(1,itype(i-2))
+ itype2=isign(10,itype(i))
+ ichir21=isign(1,itype(i))
+ ichir22=isign(1,itype(i))
+ endif
+
+ if (i.gt.3 .and. itype(i-2).ne.ntyp1) then
#ifdef OSF
phii=phi(i)
icrc=0
y(1)=0.0D0
y(2)=0.0D0
endif
- if (i.lt.nres .and. itype(i).ne.21) then
+ if (i.lt.nres .and. itype(i).ne.ntyp1) then
#ifdef OSF
phii1=phi(i+1)
icrc=0
C In following comments this theta will be referred to as t_c.
thet_pred_mean=0.0d0
do k=1,2
- athetk=athet(k,it)
- bthetk=bthet(k,it)
+ athetk=athet(k,it,ichir1,ichir2)
+ bthetk=bthet(k,it,ichir1,ichir2)
+ if (it.eq.10) then
+ athetk=athet(k,itype1,ichir11,ichir12)
+ bthetk=bthet(k,itype2,ichir21,ichir22)
+ endif
thet_pred_mean=thet_pred_mean+athetk*y(k)+bthetk*z(k)
enddo
c write (iout,*) "thet_pred_mean",thet_pred_mean
thet_pred_mean=thet_pred_mean*ss+a0thet(it)
c write (iout,*) "thet_pred_mean",thet_pred_mean
C Derivatives of the "mean" values in gamma1 and gamma2.
- dthetg1=(-athet(1,it)*y(2)+athet(2,it)*y(1))*ss
- dthetg2=(-bthet(1,it)*z(2)+bthet(2,it)*z(1))*ss
+ dthetg1=(-athet(1,it,ichir1,ichir2)*y(2)
+ &+athet(2,it,ichir1,ichir2)*y(1))*ss
+ dthetg2=(-bthet(1,it,ichir1,ichir2)*z(2)
+ & +bthet(2,it,ichir1,ichir2)*z(1))*ss
+ if (it.eq.10) then
+ dthetg1=(-athet(1,itype1,ichir11,ichir12)*y(2)
+ &+athet(2,itype1,ichir11,ichir12)*y(1))*ss
+ dthetg2=(-bthet(1,itype2,ichir21,ichir22)*z(2)
+ & +bthet(2,itype2,ichir21,ichir22)*z(1))*ss
+ endif
if (theta(i).gt.pi-delta) then
call theteng(pi-delta,thet_pred_mean,theta0(it),f0,fprim0,
& E_tc0)
etheta=0.0D0
c write (iout,*) "ithetyp",(ithetyp(i),i=1,ntyp1)
do i=ithet_start,ithet_end
- if (itype(i-1).eq.21) cycle
+ if (itype(i-1).eq.ntyp1) cycle
+ if (iabs(itype(i+1)).eq.20) iblock=2
+ if (iabs(itype(i+1)).ne.20) iblock=1
dethetai=0.0d0
dephii=0.0d0
dephii1=0.0d0
theti2=0.5d0*theta(i)
- ityp2=ithetyp(itype(i-1))
+ ityp2=ithetyp((itype(i-1)))
do k=1,nntheterm
coskt(k)=dcos(k*theti2)
sinkt(k)=dsin(k*theti2)
enddo
- if (i.gt.3 .and. itype(i-2).ne.21) then
+ if (i.gt.3 .and. itype(i-2).ne.ntyp1) then
#ifdef OSF
phii=phi(i)
if (phii.ne.phii) phii=150.0
#else
phii=phi(i)
#endif
- ityp1=ithetyp(itype(i-2))
+ ityp1=ithetyp((itype(i-2)))
do k=1,nsingle
cosph1(k)=dcos(k*phii)
sinph1(k)=dsin(k*phii)
sinph1(k)=0.0d0
enddo
endif
- if (i.lt.nres .and. itype(i).ne.21) then
+ if (i.lt.nres .and. itype(i).ne.ntyp1) then
#ifdef OSF
phii1=phi(i+1)
if (phii1.ne.phii1) phii1=150.0
#else
phii1=phi(i+1)
#endif
- ityp3=ithetyp(itype(i))
+ ityp3=ithetyp((itype(i)))
do k=1,nsingle
cosph2(k)=dcos(k*phii1)
sinph2(k)=dsin(k*phii1)
c write (iout,*) "i",i," ityp1",itype(i-2),ityp1,
c & " ityp2",itype(i-1),ityp2," ityp3",itype(i),ityp3
c call flush(iout)
- ethetai=aa0thet(ityp1,ityp2,ityp3)
+ ethetai=aa0thet(ityp1,ityp2,ityp3,iblock)
do k=1,ndouble
do l=1,k-1
ccl=cosph1(l)*cosph2(k-l)
enddo
endif
do k=1,ntheterm
- ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3)*sinkt(k)
- dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3)
+ ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3,iblock)*sinkt(k)
+ dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3,iblock)
& *coskt(k)
if (lprn)
- & write (iout,*) "k",k," aathet",aathet(k,ityp1,ityp2,ityp3),
+ & write (iout,*) "k",k,"
+ & aathet",aathet(k,ityp1,ityp2,ityp3,iblock),
& " ethetai",ethetai
enddo
if (lprn) then
endif
do m=1,ntheterm2
do k=1,nsingle
- aux=bbthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)
- & +ccthet(k,m,ityp1,ityp2,ityp3)*sinph1(k)
- & +ddthet(k,m,ityp1,ityp2,ityp3)*cosph2(k)
- & +eethet(k,m,ityp1,ityp2,ityp3)*sinph2(k)
+ aux=bbthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k)
+ & +ccthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k)
+ & +ddthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k)
+ & +eethet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k)
ethetai=ethetai+sinkt(m)*aux
dethetai=dethetai+0.5d0*m*aux*coskt(m)
dephii=dephii+k*sinkt(m)*(
- & ccthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)-
- & bbthet(k,m,ityp1,ityp2,ityp3)*sinph1(k))
+ & ccthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k)-
+ & bbthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k))
dephii1=dephii1+k*sinkt(m)*(
- & eethet(k,m,ityp1,ityp2,ityp3)*cosph2(k)-
- & ddthet(k,m,ityp1,ityp2,ityp3)*sinph2(k))
+ & eethet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k)-
+ & ddthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k))
if (lprn)
& write (iout,*) "m",m," k",k," bbthet",
- & bbthet(k,m,ityp1,ityp2,ityp3)," ccthet",
- & ccthet(k,m,ityp1,ityp2,ityp3)," ddthet",
- & ddthet(k,m,ityp1,ityp2,ityp3)," eethet",
- & eethet(k,m,ityp1,ityp2,ityp3)," ethetai",ethetai
+ & bbthet(k,m,ityp1,ityp2,ityp3,iblock)," ccthet",
+ & ccthet(k,m,ityp1,ityp2,ityp3,iblock)," ddthet",
+ & ddthet(k,m,ityp1,ityp2,ityp3,iblock)," eethet",
+ & eethet(k,m,ityp1,ityp2,ityp3,iblock)," ethetai",ethetai
enddo
enddo
if (lprn)
do m=1,ntheterm3
do k=2,ndouble
do l=1,k-1
- aux=ffthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)
+ aux=ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)
ethetai=ethetai+sinkt(m)*aux
dethetai=dethetai+0.5d0*m*coskt(m)*aux
dephii=dephii+l*sinkt(m)*(
- & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)-
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+ & -ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)-
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l))
dephii1=dephii1+(k-l)*sinkt(m)*(
- & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)-
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+ & -ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)-
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l))
if (lprn) then
write (iout,*) "m",m," k",k," l",l," ffthet",
- & ffthet(l,k,m,ityp1,ityp2,ityp3),
- & ffthet(k,l,m,ityp1,ityp2,ityp3)," ggthet",
- & ggthet(l,k,m,ityp1,ityp2,ityp3),
- & ggthet(k,l,m,ityp1,ityp2,ityp3)," ethetai",ethetai
+ & ffthet(l,k,m,ityp1,ityp2,ityp3,iblock),
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)," ggthet",
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock),
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock),
+ & " ethetai",ethetai
write (iout,*) cosph1ph2(l,k)*sinkt(m),
& cosph1ph2(k,l)*sinkt(m),
& sinph1ph2(l,k)*sinkt(m),sinph1ph2(k,l)*sinkt(m)
c write (iout,'(a)') 'ESC'
do i=loc_start,loc_end
it=itype(i)
- if (it.eq.21) cycle
+ if (it.eq.ntyp1) cycle
if (it.eq.10) goto 1
- nlobit=nlob(it)
+ nlobit=nlob(iabs(it))
c print *,'i=',i,' it=',it,' nlobit=',nlobit
c write (iout,*) 'i=',i,' ssa=',ssa,' ssad=',ssad
theti=theta(i+1)-pipol
do iii=-1,1
do j=1,nlobit
- expfac=dexp(bsc(j,it)-0.5D0*contr(j,iii)+emin)
+ expfac=dexp(bsc(j,iabs(it))-0.5D0*contr(j,iii)+emin)
cd print *,'j=',j,' expfac=',expfac
escloc_i=escloc_i+expfac
do k=1,3
dersc12=0.0d0
do j=1,nlobit
- expfac=dexp(bsc(j,it)-0.5D0*contr(j)+emin)
+ expfac=dexp(bsc(j,iabs(it))-0.5D0*contr(j)+emin)
escloc_i=escloc_i+expfac
do k=1,2
dersc(k)=dersc(k)+Ax(k,j)*expfac
delta=0.02d0*pi
escloc=0.0D0
do i=loc_start,loc_end
- if (itype(i).eq.21) cycle
+ if (itype(i).eq.ntyp1) cycle
costtab(i+1) =dcos(theta(i+1))
sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
cosfac=dsqrt(cosfac2)
sinfac2=0.5d0/(1.0d0-costtab(i+1))
sinfac=dsqrt(sinfac2)
- it=itype(i)
+ it=iabs(itype(i))
if (it.eq.10) goto 1
c
C Compute the axes of tghe local cartesian coordinates system; store in
y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
enddo
do j = 1,3
- z_prime(j) = -uz(j,i-1)
+ z_prime(j) = -uz(j,i-1)*dsign(1.0d0,dfloat(itype(i)))
enddo
c write (2,*) "i",i
c write (2,*) "x_prime",(x_prime(j),j=1,3)
C Compute the energy of the ith side cbain
C
c write (2,*) "xx",xx," yy",yy," zz",zz
- it=itype(i)
+ it=iabs(itype(i))
do j = 1,65
x(j) = sc_parmin(j,it)
enddo
Cc diagnostics - remove later
xx1 = dcos(alph(2))
yy1 = dsin(alph(2))*dcos(omeg(2))
- zz1 = -dsin(alph(2))*dsin(omeg(2))
+ zz1 = -dsign(1.0d0,itype(i))*dsin(alph(2))*dsin(omeg(2))
write(2,'(3f8.1,3f9.3,1x,3f9.3)')
& alph(2)*rad2deg,omeg(2)*rad2deg,theta(3)*rad2deg,xx,yy,zz,
& xx1,yy1,zz1
c sumene = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
escloc = escloc + sumene
c write (2,*) "escloc",escloc
+c write (2,*) "i",i," escloc",sumene,escloc,it,itype(i),
+c & zz,xx,yy
if (.not. calc_grad) goto 1
#ifdef DEBUG
C
dZZ_Ci1(k)=0.0d0
dZZ_Ci(k)=0.0d0
do j=1,3
- dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)*dC_norm(j,i+nres)
- dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)*dC_norm(j,i+nres)
+ dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)
+ & *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres)
+ dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)
+ & *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres)
enddo
dXX_XYZ(k)=vbld_inv(i+nres)*(x_prime(k)-xx*dC_norm(k,i+nres))
c lprn=.true.
etors=0.0D0
do i=iphi_start,iphi_end
- if (itype(i-2).eq.21 .or. itype(i-1).eq.21
- & .or. itype(i).eq.21) cycle
+ if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1
+ & .or. itype(i).eq.ntyp1) cycle
itori=itortyp(itype(i-2))
itori1=itortyp(itype(i-1))
phii=phi(i)
c lprn=.true.
etors=0.0D0
do i=iphi_start,iphi_end
- if (itype(i-2).eq.21 .or. itype(i-1).eq.21
- & .or. itype(i).eq.21) cycle
+ if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1
+ & .or. itype(i).eq.ntyp1) cycle
if (itel(i-2).eq.0 .or. itel(i-1).eq.0) goto 1215
+ if (iabs(itype(i)).eq.20) then
+ iblock=2
+ else
+ iblock=1
+ endif
itori=itortyp(itype(i-2))
itori1=itortyp(itype(i-1))
phii=phi(i)
gloci=0.0D0
C Regular cosine and sine terms
- do j=1,nterm(itori,itori1)
- v1ij=v1(j,itori,itori1)
- v2ij=v2(j,itori,itori1)
+ do j=1,nterm(itori,itori1,iblock)
+ v1ij=v1(j,itori,itori1,iblock)
+ v2ij=v2(j,itori,itori1,iblock)
cosphi=dcos(j*phii)
sinphi=dsin(j*phii)
etors=etors+v1ij*cosphi+v2ij*sinphi
C
cosphi=dcos(0.5d0*phii)
sinphi=dsin(0.5d0*phii)
- do j=1,nlor(itori,itori1)
+ do j=1,nlor(itori,itori1,iblock)
vl1ij=vlor1(j,itori,itori1)
vl2ij=vlor2(j,itori,itori1)
vl3ij=vlor3(j,itori,itori1)
pom=vl2ij*cosphi+vl3ij*sinphi
pom1=1.0d0/(pom*pom+1.0d0)
etors=etors+vl1ij*pom1
+c if (energy_dec) etors_ii=etors_ii+
+c & vl1ij*pom1
pom=-pom*pom1*pom1
gloci=gloci+vl1ij*(vl3ij*cosphi-vl2ij*sinphi)*pom
enddo
C Subtract the constant term
- etors=etors-v0(itori,itori1)
+ etors=etors-v0(itori,itori1,iblock)
if (lprn)
& write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)')
& restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
- & (v1(j,itori,itori1),j=1,6),(v2(j,itori,itori1),j=1,6)
+ & (v1(j,itori,itori1,1),j=1,6),(v2(j,itori,itori1,1),j=1,6)
gloc(i-3,icg)=gloc(i-3,icg)+wtor*fact*gloci
c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg)
1215 continue
c lprn=.true.
etors_d=0.0D0
do i=iphi_start,iphi_end-1
- if (itype(i-2).eq.21 .or. itype(i-1).eq.21
- & .or. itype(i).eq.21 .or. itype(i+1).eq.21) cycle
+ if (itype(i-2).eq.ntyp1.or. itype(i-1).eq.ntyp1
+ & .or. itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
if (itel(i-2).eq.0 .or. itel(i-1).eq.0 .or. itel(i).eq.0)
& goto 1215
itori=itortyp(itype(i-2))
phii1=phi(i+1)
gloci1=0.0D0
gloci2=0.0D0
+ iblock=1
+ if (iabs(itype(i+1)).eq.20) iblock=2
C Regular cosine and sine terms
- do j=1,ntermd_1(itori,itori1,itori2)
- v1cij=v1c(1,j,itori,itori1,itori2)
- v1sij=v1s(1,j,itori,itori1,itori2)
- v2cij=v1c(2,j,itori,itori1,itori2)
- v2sij=v1s(2,j,itori,itori1,itori2)
+ do j=1,ntermd_1(itori,itori1,itori2,iblock)
+ v1cij=v1c(1,j,itori,itori1,itori2,iblock)
+ v1sij=v1s(1,j,itori,itori1,itori2,iblock)
+ v2cij=v1c(2,j,itori,itori1,itori2,iblock)
+ v2sij=v1s(2,j,itori,itori1,itori2,iblock)
cosphi1=dcos(j*phii)
sinphi1=dsin(j*phii)
cosphi2=dcos(j*phii1)
gloci1=gloci1+j*(v1sij*cosphi1-v1cij*sinphi1)
gloci2=gloci2+j*(v2sij*cosphi2-v2cij*sinphi2)
enddo
- do k=2,ntermd_2(itori,itori1,itori2)
+ do k=2,ntermd_2(itori,itori1,itori2,iblock)
do l=1,k-1
- v1cdij = v2c(k,l,itori,itori1,itori2)
- v2cdij = v2c(l,k,itori,itori1,itori2)
- v1sdij = v2s(k,l,itori,itori1,itori2)
- v2sdij = v2s(l,k,itori,itori1,itori2)
+ v1cdij = v2c(k,l,itori,itori1,itori2,iblock)
+ v2cdij = v2c(l,k,itori,itori1,itori2,iblock)
+ v1sdij = v2s(k,l,itori,itori1,itori2,iblock)
+ v2sdij = v2s(l,k,itori,itori1,itori2,iblock)
cosphi1p2=dcos(l*phii+(k-l)*phii1)
cosphi1m2=dcos(l*phii-(k-l)*phii1)
sinphi1p2=dsin(l*phii+(k-l)*phii1)
gloci1=gloci1+l*(v1sdij*cosphi1p2+v2sdij*cosphi1m2
& -v1cdij*sinphi1p2-v2cdij*sinphi1m2)
gloci2=gloci2+(k-l)*(v1sdij*cosphi1p2-v2sdij*cosphi1m2
- & -v1cdij*sinphi1p2+v2cdij*sinphi1m2)
+ & -v1cdij*sinphi1p2+v2cdij*sinphi1m2)
enddo
enddo
gloc(i-3,icg)=gloc(i-3,icg)+wtor_d*fact2*gloci1
c lprn=.true.
c write (iout,*) "EBACK_SC_COR",iphi_start,iphi_end,nterm_sccor
esccor=0.0D0
- do i=iphi_start,iphi_end
- if (itype(i-2).eq.21 .or. itype(i-1).eq.21) cycle
+ do i=itau_start,itau_end
+ if ((itype(i-2).eq.ntyp1).or.(itype(i-1).eq.ntyp1)) cycle
esccor_ii=0.0D0
- itori=itype(i-2)
- itori1=itype(i-1)
+ isccori=isccortyp(itype(i-2))
+ isccori1=isccortyp(itype(i-1))
phii=phi(i)
+ do intertyp=1,3 !intertyp
+cc Added 09 May 2012 (Adasko)
+cc Intertyp means interaction type of backbone mainchain correlation:
+c 1 = SC...Ca...Ca...Ca
+c 2 = Ca...Ca...Ca...SC
+c 3 = SC...Ca...Ca...SCi
gloci=0.0D0
- do j=1,nterm_sccor
- v1ij=v1sccor(j,itori,itori1)
- v2ij=v2sccor(j,itori,itori1)
- cosphi=dcos(j*phii)
- sinphi=dsin(j*phii)
- esccor=esccor+v1ij*cosphi+v2ij*sinphi
- gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
- enddo
+ if (((intertyp.eq.3).and.((itype(i-2).eq.10).or.
+ & (itype(i-1).eq.10).or.(itype(i-2).eq.ntyp1).or.
+ & (itype(i-1).eq.ntyp1)))
+ & .or. ((intertyp.eq.1).and.((itype(i-2).eq.10)
+ & .or.(itype(i-2).eq.ntyp1).or.(itype(i-1).eq.ntyp1)
+ & .or.(itype(i).eq.ntyp1)))
+ & .or.((intertyp.eq.2).and.((itype(i-1).eq.10).or.
+ & (itype(i-1).eq.ntyp1).or.(itype(i-2).eq.ntyp1).or.
+ & (itype(i-3).eq.ntyp1)))) cycle
+ if ((intertyp.eq.2).and.(i.eq.4).and.(itype(1).eq.ntyp1)) cycle
+ if ((intertyp.eq.1).and.(i.eq.nres).and.(itype(nres).eq.ntyp1))
+ & cycle
+ do j=1,nterm_sccor(isccori,isccori1)
+ v1ij=v1sccor(j,intertyp,isccori,isccori1)
+ v2ij=v2sccor(j,intertyp,isccori,isccori1)
+ cosphi=dcos(j*tauangle(intertyp,i))
+ sinphi=dsin(j*tauangle(intertyp,i))
+ esccor=esccor+v1ij*cosphi+v2ij*sinphi
+ gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
+ enddo
+c write (iout,*) "EBACK_SC_COR",i,v1ij*cosphi+v2ij*sinphi,intertyp,
+c & nterm_sccor(isccori,isccori1),isccori,isccori1
+c gloc_sc(intertyp,i-3,icg)=gloc_sc(intertyp,i-3,icg)+wsccor*gloci
if (lprn)
& write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)')
& restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
- & (v1sccor(j,itori,itori1),j=1,6),(v2sccor(j,itori,itori1),j=1,6)
- gsccor_loc(i-3)=gloci
+ & (v1sccor(j,1,itori,itori1),j=1,6)
+ & ,(v2sccor(j,1,itori,itori1),j=1,6)
+c gsccor_loc(i-3)=gloci
+ enddo !intertyp
enddo
return
end
integer dimen1,dimen2,atom,indx
double precision buffer(dimen1,dimen2)
double precision zapas
- common /contacts_hb/ zapas(3,20,maxres,7),
- & facont_hb(20,maxres),ees0p(20,maxres),ees0m(20,maxres),
- & num_cont_hb(maxres),jcont_hb(20,maxres)
+ common /contacts_hb/ zapas(3,ntyp,maxres,7),
+ & facont_hb(ntyp,maxres),ees0p(ntyp,maxres),ees0m(ntyp,maxres),
+ & num_cont_hb(maxres),jcont_hb(ntyp,maxres)
num_kont=num_cont_hb(atom)
do i=1,num_kont
do k=1,7
integer dimen1,dimen2,atom,indx
double precision buffer(dimen1,dimen2)
double precision zapas
- common /contacts_hb/ zapas(3,20,maxres,7),
- & facont_hb(20,maxres),ees0p(20,maxres),ees0m(20,maxres),
- & num_cont_hb(maxres),jcont_hb(20,maxres)
+ common /contacts_hb/ zapas(3,ntyp,maxres,7),
+ & facont_hb(ntyp,maxres),ees0p(ntyp,maxres),
+ & ees0m(ntyp,maxres),
+ & num_cont_hb(maxres),jcont_hb(ntyp,maxres)
num_kont=buffer(1,indx+26)
num_kont_old=num_cont_hb(atom)
num_cont_hb(atom)=num_kont+num_kont_old
include 'COMMON.GEO'
logical swap
double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2),
- & auxvec1(2),auxvec2(1),auxmat1(2,2)
+ & auxvec1(2),auxvec2(2),auxmat1(2,2)
logical lprn
common /kutas/ lprn
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
& vbldsc0_all(maxbondterm,ntyp,max_parm),
& aksc_all(maxbondterm,ntyp,max_parm),
& abond0_all(maxbondterm,ntyp,max_parm),
- & a0thet_all(ntyp,max_parm),athet_all(2,ntyp,max_parm),
- & bthet_all(2,ntyp,max_parm),polthet_all(0:3,ntyp,max_parm),
- & gthet_all(3,ntyp,max_parm),theta0_all(ntyp,max_parm),
- & sig0_all(ntyp,max_parm),sigc0_all(ntyp,max_parm),
+ & a0thet_all(-ntyp:ntyp,max_parm),
+ & athet_all(2,-ntyp:ntyp,-1:1,-1:1,max_parm),
+ & bthet_all(2,-ntyp:ntyp,-1:1,-1:1,max_parm),
+ & polthet_all(0:3,-ntyp:ntyp,max_parm),
+ & gthet_all(3,-ntyp:ntyp,max_parm),theta0_all(-ntyp:ntyp,max_parm),
+ & sig0_all(-ntyp:ntyp,max_parm),sigc0_all(-ntyp:ntyp,max_parm),
& aa0thet_all(maxthetyp1,maxthetyp1,maxthetyp1,max_parm),
& aathet_all(maxtheterm,maxthetyp1,maxthetyp1,maxthetyp1,max_parm),
& bbthet_all(maxsingle,maxtheterm2,maxthetyp1,maxthetyp1,
& ggthet_all(maxdouble,maxdouble,maxtheterm3,maxthetyp1,maxthetyp1,
& maxthetyp1,max_parm),
& dsc_all(ntyp1,max_parm),bsc_all(maxlob,ntyp,max_parm),
- & censc_all(3,maxlob,ntyp,max_parm),
- & gaussc_all(3,3,maxlob,ntyp,max_parm),dsc0_all(ntyp1,max_parm),
+ & censc_all(3,maxlob,-ntyp:ntyp,max_parm),
+ & gaussc_all(3,3,maxlob,-ntyp:ntyp,max_parm),
+ & dsc0_all(ntyp1,max_parm),
& sc_parmin_all(65,ntyp,max_parm),
- & v0_all(maxtor,maxtor,max_parm),
- & v1_all(maxterm,maxtor,maxtor,max_parm),
- & v2_all(maxterm,maxtor,maxtor,max_parm),
+ & v0_all(-maxtor:maxtor,-maxtor:maxtor,2,max_parm),
+ & v1_all(maxterm,-maxtor:maxtor,-maxtor:maxtor,2,max_parm),
+ & v2_all(maxterm,-maxtor:maxtor,-maxtor:maxtor,2,max_parm),
& vlor1_all(maxlor,maxtor,maxtor,max_parm),
& vlor2_all(maxlor,maxtor,maxtor,max_parm),
& vlor3_all(maxlor,maxtor,maxtor,max_parm),
- & v1c_all(2,maxtermd_1,maxtor,maxtor,maxtor,max_parm),
- & v1s_all(2,maxtermd_1,maxtor,maxtor,maxtor,max_parm),
- & v2c_all(maxtermd_2,maxtermd_2,maxtor,maxtor,maxtor,max_parm),
- & v2s_all(maxtermd_2,maxtermd_2,maxtor,maxtor,maxtor,max_parm),
- & b1_all(2,maxtor,max_parm),b2_all(2,maxtor,max_parm),
- & cc_all(2,2,maxtor,max_parm),dd_all(2,2,maxtor,max_parm),
- & ee_all(2,2,maxtor,max_parm),ctilde_all(2,2,maxtor,max_parm),
- & dtilde_all(2,2,maxtor,max_parm),b1tilde_all(2,maxtor,max_parm),
+ & v1c_all(2,maxtermd_1,-maxtor:maxtor,-maxtor:maxtor,
+ & -maxtor:maxtor,2,max_parm),
+ & v1s_all(2,maxtermd_1,-maxtor:maxtor,-maxtor:maxtor,
+ & -maxtor:maxtor,2,max_parm),
+ & v2c_all(maxtermd_2,maxtermd_2,-maxtor:maxtor,
+ & -maxtor:maxtor,-maxtor:maxtor,2,max_parm),
+ & v2s_all(maxtermd_2,maxtermd_2,-maxtor:maxtor,-maxtor:maxtor,
+ & -maxtor:maxtor,2,max_parm),
+ & b1_all(2,-maxtor:maxtor,max_parm),
+ & b2_all(2,-maxtor:maxtor,max_parm),
+ & cc_all(2,2,-maxtor:maxtor,max_parm),
+ & dd_all(2,2,-maxtor:maxtor,max_parm),
+ & ee_all(2,2,-maxtor:maxtor,max_parm),
+ & ctilde_all(2,2,-maxtor:maxtor,max_parm),
+ & dtilde_all(2,2,-maxtor:maxtor,max_parm),
+ & b1tilde_all(2,-maxtor:maxtor,max_parm),
& app_all(2,2,max_parm),bpp_all(2,2,max_parm),
& ael6_all(2,2,max_parm),ael3_all(2,2,max_parm),
& aad_all(ntyp,2,max_parm),bad_all(ntyp,2,max_parm),
& sigma_all(ntyp,ntyp,max_parm),r0_all(ntyp,ntyp,max_parm),
& chi_all(ntyp,ntyp,max_parm),chip_all(ntyp,max_parm),
& alp_all(ntyp,max_parm),ebr_all(max_parm),d0cm_all(max_parm),
+ & ss_depth_all(max_parm),ht_all(max_parm),
& akcm_all(max_parm),akth_all(max_parm),akct_all(max_parm),
& v1ss_all(max_parm),v2ss_all(max_parm),v3ss_all(max_parm),
& v1sccor_all(maxterm_sccor,3,ntyp,ntyp,max_parm),
& v2sccor_all(maxterm_sccor,3,ntyp,ntyp,max_parm)
- integer nlob_all(ntyp1,max_parm),nlor_all(maxtor,maxtor,max_parm),
- & nterm_all(maxtor,maxtor,max_parm),
- & ntermd1_all(maxtor,maxtor,maxtor,max_parm),
- & ntermd2_all(maxtor,maxtor,maxtor,max_parm),
+ integer nlob_all(ntyp1,max_parm),
+ & nlor_all(-maxtor:maxtor,-maxtor:maxtor,2,max_parm),
+ & nterm_all(-maxtor:maxtor,-maxtor:maxtor,2,max_parm),
+ & ntermd1_all(-maxtor:maxtor,-maxtor:maxtor,
+ & -maxtor:maxtor,2,max_parm),
+ & ntermd2_all(-maxtor:maxtor,-maxtor:maxtor,
+ & -maxtor:maxtor,2,max_parm),
& nbondterm_all(ntyp,max_parm),nthetyp_all(max_parm),
& ithetyp_all(ntyp1,max_parm),ntheterm_all(max_parm),
& ntheterm2_all(max_parm),ntheterm3_all(max_parm),
& ctilde_all,dtilde_all,b1tilde_all,app_all,bpp_all,ael6_all,
& ael3_all,aad_all,bad_all,aa_all,bb_all,augm_all,
& eps_all,sigma_all,r0_all,chi_all,chip_all,alp_all,ebr_all,
+ & ss_depth_all,ht_all,
& d0cm_all,akcm_all,akth_all,akct_all,v1ss_all,v2ss_all,v3ss_all,
& v1sccor_all,v2sccor_all,nbondterm_all,
& nlob_all,nlor_all,nterm_all,ntermd1_all,ntermd2_all,
& ((csingle(l,k+nres),l=1,3),k=nnt,nct),
& nss,(ihpb(k),jhpb(k),k=1,nss),
& eini,efree,rmsdev,(q(j,iii+1),j=1,nQ),iR,ib,ipar
+ cc write(iout,*), 'NAWEJ',i,eini
if (indpdb.gt.0) then
do k=1,nres
do l=1,3
& " the value read in: ",energia(0),eini," point",
& iii+1,indstart(me1)+iii," T",
& 1.0d0/(1.987D-3*beta_h(ib,ipar))
- errmsg_count=errmsg_count+1
+ call enerprint(energia(0),fT)
+ call pdbout(iii+1,beta_h(ib,ipar),
+ & eini,energia(0),0.0d0,rmsdev)
+ write (iout,*)
+ errmsg_count=errmsg_count+1
+ call pdbout(indstart(me1)+iii,
+ & 1.0d0/(1.987D-3*beta_h(ib,ipar)),
+ &energia(0),eini,0.0d0,0.0d0)
+ call enerprint(energia(0),fT)
if (errmsg_count.gt.maxerrmsg_count)
& write (iout,*) "Too many warning messages"
if (einicheck.gt.1) then
do k=1,21
enetb(k,iii+1,iparm)=energia(k)
enddo
+ c write(iout,*) "iCHUJ TU STRZELI",i,iii,entfac(i)
+ c call enerprint(energia(0),fT)
#ifdef DEBUG
write (iout,'(2i5,f10.1,3e15.5)') i,iii,
& 1.0d0/(beta_h(ib,ipar)*1.987D-3),energia(0),eini,efree
- c call enerprint(energia(0),fT)
- #endif
- #ifdef DEBUG
+ call enerprint(energia(0),fT)
write (iout,'(8f10.5)') ((c(l,k),l=1,3),k=1,nres)
write (iout,'(8f10.5)') ((c(l,k+nres),l=1,3),k=nnt,nct)
write (iout,'(8f10.4)') (vbld(k),k=nnt+1,nct)
write (iout,'(8f10.5)') (q(k,iii+1),k=1,nQ)
write (iout,'(f10.5,i10)') rmsdev,iscor
call enerprint(energia(0),fT)
+ write(liczba,'(bz,i3.3)') me
+ nazwa="test"//liczba//".pdb"
+ write (iout,*) "pdb file",nazwa
+ open (ipdb,file=nazwa,position="append")
call pdbout(ii+1,beta_h(ib,ipar),efree,energia(0),0.0d0,rmsdev)
+ close(ipdb)
#endif
endif
#else
do i=1,ntot(islice)
#endif
+ cc if (dyn_ss) then
+ cc read(ientout,rec=i,err=101)
+ cc & ((csingle(l,k),l=1,3),k=1,nres),
+ cc & ((csingle(l,k+nres),l=1,3),k=nnt,nct),
+ cc & nss,(idssb(k),jdssb(k),k=1,nss),
+ cc & eini,efree,rmsdev,(q(k,i),k=1,nQ),iR,ib,iparm
+ cc idssb(k)=idssb(k)-nres
+ cc jdssb(k)=jdssb(k)-nres
+ cc else
read(ientout,rec=i,err=101)
& ((csingle(l,k),l=1,3),k=1,nres),
& ((csingle(l,k+nres),l=1,3),k=nnt,nct),
& nss,(ihpb(k),jhpb(k),k=1,nss),
& eini,efree,rmsdev,(q(k,i),k=1,nQ),iR,ib,iparm
- c write (iout,*) iR,ib,iparm,eini,efree
+ cc endif
+ cc write (iout,*) 'CC', iR,ib,iparm,eini,efree
do j=1,2*nres
do k=1,3
c(k,j)=csingle(k,j)
iscore=0
if (indpdb.gt.0) then
call conf_compar(i,.false.,.true.)
- endif
+ endif
+ c if (dyn_ss) then
if (bxfile .or.cxfile .or. ensembles.gt.0) write (ientin,rec=i)
& ((csingle(l,k),l=1,3),k=1,nres),
& ((csingle(l,k+nres),l=1,3),k=nnt,nct),
& nss,(ihpb(k),jhpb(k),k=1,nss),
c & potE(i,iparm),-entfac(i),rms_nat,iscore
& potE(i,nparmset),-entfac(i),rms_nat,iscore
- c write (iout,'(2i5,3e15.5)') i,me,potE(i,iparm),-entfac(i)
+ c else
+ if (bxfile .or.cxfile .or. ensembles.gt.0) write
+ & (ientin,rec=i)
+ & ((csingle(l,k),l=1,3),k=1,nres),
+ & ((csingle(l,k+nres),l=1,3),k=nnt,nct),
+ & nss,(ihpb(k),jhpb(k),k=1,nss),
+ c & potE(i,iparm),-entfac(i),rms_nat,iscore
+ & potE(i,nparmset),-entfac(i),rms_nat,iscore
+ c endif
+ write (iout,'(2i5,3e15.5)') i,me,potE(i,iparm),-entfac(i)
#ifndef MPI
if (cxfile) call cxwrite(ixdrf,csingle,potE(i,nparmset),
& -entfac(i),rms_nat,iscore)
c call flush(iout)
do i=indstart(j),indend(j)
iii = iii+1
+ cc if (dyn_ss) then
+ cc read(ientin,rec=iii,err=101)
+ cc & ((csingle(l,k),l=1,3),k=1,nres),
+ cc & ((csingle(l,k+nres),l=1,3),k=nnt,nct),
+ cc & nss,(idssb(k),jdssb(k),k=1,nss),
+ cc & eini,efree,rmsdev,iscor
+ cc idssb(k)=idssb(k)-nres
+ cc jdssb(k)=jdssb(k)-nres
+ cc else
read(ientin,rec=iii,err=101)
& ((csingle(l,k),l=1,3),k=1,nres),
& ((csingle(l,k+nres),l=1,3),k=nnt,nct),
& nss,(ihpb(k),jhpb(k),k=1,nss),
& eini,efree,rmsdev,iscor
+ cc endif
if (bxfile .or. ensembles.gt.0) then
- write (ientout,rec=i)
+ cc if (dyn_ss) then
+ cc write (ientout,rec=i)
+ cc & ((csingle(l,k),l=1,3),k=1,nres),
+ cc & ((csingle(l,k+nres),l=1,3),k=nnt,nct),
+ cc & nss,(idssb(k)+nres,jdssb(k)+nres,k=1,nss),
+ cc & eini,efree,rmsdev,iscor
+ cc else
+ write (ientout,rec=i)
& ((csingle(l,k),l=1,3),k=1,nres),
& ((csingle(l,k+nres),l=1,3),k=nnt,nct),
& nss,(ihpb(k),jhpb(k),k=1,nss),
& eini,efree,rmsdev,iscor
+ cc write(iout,*) "W poszukiwaniu zlotych galotow"
+ cc write(iout,*) "efree=",efree,iii
+ cc endif
endif
if(cxfile)call cxwrite(ixdrf,csingle,eini,efree,rmsdev,iscor)
#ifdef DEBUG
c write (iout,*) "itmp",itmp
c call flush(iout)
+ c write (iout,*) "CNZ",eini,dyn_ss
#if (defined(AIX) && !defined(JUBL))
call xdrf3dfcoord_(ixdrf, xoord, itmp, prec, iret)
c call flush(iout)
call xdrfint_(ixdrf, nss, iret)
do j=1,nss
+ cc if (dyn_ss) then
+ cc call xdrfint_(ixdrf, idssb(j)+nres, iret)
+ cc call xdrfint_(ixdrf, jdssb(j)+nres, iret)
+ cc else
call xdrfint_(ixdrf, ihpb(j), iret)
call xdrfint_(ixdrf, jhpb(j), iret)
+ cc endif
enddo
call xdrffloat_(ixdrf,real(eini),iret)
call xdrffloat_(ixdrf,real(efree),iret)
call xdrfint(ixdrf, nss, iret)
do j=1,nss
+ cc if (dyn_ss) then
+ cc call xdrfint(ixdrf, idssb(j), iret)
+ cc call xdrfint(ixdrf, jdssb(j), iret)
+ cc idssb(j)=idssb(j)-nres
+ cc jdssb(j)=jdssb(j)-nres
+ cc else
call xdrfint(ixdrf, ihpb(j), iret)
call xdrfint(ixdrf, jhpb(j), iret)
+ cc endif
enddo
call xdrffloat(ixdrf,real(eini),iret)
- call xdrffloat(ixdrf,real(efree),iret)
+ call xdrffloat(ixdrf,real(efree),iret)
call xdrffloat(ixdrf,real(rmsdev),iret)
call xdrfint(ixdrf,iscor,iret)
#endif
enddo
do j=nnt,nct
itj=itype(j)
- if (itype(j).ne.10 .and. (vbld(nres+j)-dsc(itj)).gt.2.0d0) then
+ if (itype(j).ne.10 .and.(vbld(nres+j)-dsc(iabs(itj))).gt.2.0d0)
+ & then
if (iprint.gt.0)
& write (iout,*) "Bad CA-SC bond length",j," ",vbld(nres+j),
& " for conformation",ii
etot=wsc*(evdw+fact(6)*evdw_t)+wscp*evdw2+welec*fact(1)*ees
& +wvdwpp*evdw1
& +wang*ebe+wtor*fact(1)*etors+wscloc*escloc
- & +wstrain*ehpb+nss*ebr+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5
+ & +wstrain*ehpb+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5
& +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4
& +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6
& +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d
etot=wsc*(evdw+fact(6)*evdw_t)+wscp*evdw2
& +welec*fact(1)*(ees+evdw1)
& +wang*ebe+wtor*fact(1)*etors+wscloc*escloc
- & +wstrain*ehpb+nss*ebr+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5
+ & +wstrain*ehpb+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5
& +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4
& +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6
& +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d
energia(19)=esccor
energia(20)=edihcnstr
energia(21)=evdw_t
+ c if (dyn_ss) call dyn_set_nss
c detecting NaNQ
#ifdef ISNAN
#ifdef AIX
& +wturn3*fact(2)*gel_loc_turn3(i)
& +wturn6*fact(5)*gel_loc_turn6(i)
& +wel_loc*fact(2)*gel_loc_loc(i)
- & +wsccor*fact(1)*gsccor_loc(i)
+c & +wsccor*fact(1)*gsccor_loc(i)
enddo
endif
return
evdw=0.0D0
evdw_t=0.0d0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
cd write (iout,*) 'i=',i,' iint=',iint,' istart=',istart(i,iint),
cd & 'iend=',iend(i,iint)
do j=istart(i,iint),iend(i,iint)
- itypj=itype(j)
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
zj=c(3,nres+j)-zi
evdw=0.0D0
evdw_t=0.0d0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
C
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
- itypj=itype(j)
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
zj=c(3,nres+j)-zi
c endif
ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
ind=ind+1
- itypj=itype(j)
+ itypj=iabs(itype(j))
dscj_inv=vbld_inv(j+nres)
chi1=chi(itypi,itypj)
chi2=chi(itypj,itypi)
include 'COMMON.ENEPS'
include 'COMMON.IOUNITS'
include 'COMMON.CALC'
+ include 'COMMON.SBRIDGE'
logical lprn
common /srutu/icall
integer icant
c if (icall.gt.0) lprn=.true.
ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
C
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
+ C in case of diagnostics write (iout,*) "TU SZUKAJ",i,j,dyn_ss_mask(i),dyn_ss_mask(j)
+ C /06/28/2013 Adasko: In case of dyn_ss - dynamic disulfide bond
+ C formation no electrostatic interactions should be calculated. If it
+ C would be allowed NaN would appear
+ IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN
+ C /06/28/2013 Adasko: dyn_ss_mask is logical statement wheather this Cys
+ C residue can or cannot form disulfide bond. There is still bug allowing
+ C Cys...Cys...Cys bond formation
+ call dyn_ssbond_ene(i,j,evdwij)
+ C /06/28/2013 Adasko: dyn_ssbond_ene is dynamic SS bond foration energy
+ C function in ssMD.F
+ evdw=evdw+evdwij
+ c if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)')
+ c & 'evdw',i,j,evdwij,' ss'
+ ELSE
ind=ind+1
- itypj=itype(j)
+ itypj=iabs(itype(j))
dscj_inv=vbld_inv(j+nres)
sig0ij=sigma(itypi,itypj)
chi1=chi(itypi,itypj)
c write (iout,*) "i",i," j",j," itypi",itypi," itypj",itypj,
c & " ij",ij," eneps",aux*e1/dabs(eps(itypi,itypj)),
c & aux*e2/eps(itypi,itypj)
+ c write (iout,'(a6,2i5,0pf7.3)') 'evdw',i,j,evdwij
if (lprn) then
sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
C Calculate angular part of the gradient.
call sc_grad
endif
+ ENDIF ! dyn_ss
enddo ! j
enddo ! iint
enddo ! i
c if (icall.gt.0) lprn=.true.
ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
ind=ind+1
- itypj=itype(j)
+ itypj=iabs(itype(j))
dscj_inv=vbld_inv(j+nres)
sig0ij=sigma(itypi,itypj)
r0ij=r0(itypi,itypj)
do iint=1,nscp_gr(i)
do j=iscpstart(i,iint),iscpend(i,iint)
- itypj=itype(j)
+ itypj=iabs(itype(j))
C Uncomment following three lines for SC-p interactions
c xj=c(1,nres+j)-xi
c yj=c(2,nres+j)-yi
c & dhpb(i),dhpb1(i),forcon(i)
C 24/11/03 AL: SS bridges handled separately because of introducing a specific
C distance and angle dependent SS bond potential.
- if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and.
+ if (.not.dyn_ss .and. i.le.nss) then
+ C 15/02/13 CC dynamic SSbond - additional check
- if (ii.gt.nres .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then
++ if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and.
+ & iabs(itype(jjj)).eq.1) then
call ssbond_ene(iii,jjj,eij)
ehpb=ehpb+2*eij
+ endif
cd write (iout,*) "eij",eij
else if (ii.gt.nres .and. jj.gt.nres) then
c Restraints from contact prediction
include 'COMMON.VAR'
include 'COMMON.IOUNITS'
double precision erij(3),dcosom1(3),dcosom2(3),gg(3)
- itypi=itype(i)
+ itypi=iabs(itype(i))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
dyi=dc_norm(2,nres+i)
dzi=dc_norm(3,nres+i)
dsci_inv=dsc_inv(itypi)
- itypj=itype(j)
+ itypj=iabs(itype(j))
dscj_inv=dsc_inv(itypj)
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
deltat12=om2-om1+2.0d0
cosphi=om12-om1*om2
eij=akcm*deltad*deltad+akth*(deltat1*deltat1+deltat2*deltat2)
- & +akct*deltad*deltat12
+ & +akct*deltad*deltat12+ebr
+ c & +akct*deltad*deltat12
& +v1ss*cosphi+v2ss*cosphi*cosphi+v3ss*cosphi*cosphi*cosphi
- c write(iout,*) i,j,"rij",rij,"d0cm",d0cm," akcm",akcm," akth",akth,
- c & " akct",akct," deltad",deltad," deltat",deltat1,deltat2,
- c & " deltat12",deltat12," eij",eij
+ write(iout,*) i,j,"rij",rij,"d0cm",d0cm," akcm",akcm," akth",akth,
+ & " akct",akct," deltad",deltad," deltat",deltat1,deltat2,
+ & " deltat12",deltat12," eij",eij,"ebr",ebr
ed=2*akcm*deltad+akct*deltat12
pom1=akct*deltad
pom2=v1ss+2*v2ss*cosphi+3*v3ss*cosphi*cosphi
include 'COMMON.FFIELD'
include 'COMMON.CONTROL'
double precision u(3),ud(3)
+ logical :: lprn=.false.
estr=0.0d0
do i=nnt+1,nct
diff = vbld(i)-vbldp0
c 09/18/07 AL: multimodal bond potential based on AM1 CA-SC PMF's included
c
do i=nnt,nct
- iti=itype(i)
+ iti=iabs(itype(i))
if (iti.ne.10) then
nbi=nbondterm(iti)
if (nbi.eq.1) then
diff=vbld(i+nres)-vbldsc0(1,iti)
- c write (iout,*) i,iti,vbld(i+nres),vbldsc0(1,iti),diff,
- c & AKSC(1,iti),AKSC(1,iti)*diff*diff
+ if (lprn)
+ & write (iout,*) i,iti,vbld(i+nres),vbldsc0(1,iti),diff,
+ & AKSC(1,iti),AKSC(1,iti)*diff*diff
estr=estr+0.5d0*AKSC(1,iti)*diff*diff
do j=1,3
gradbx(j,i)=AKSC(1,iti)*diff*dc(j,i+nres)/vbld(i+nres)
usum=usum+uprod1
usumsqder=usumsqder+ud(j)*uprod2
enddo
- c write (iout,*) i,iti,vbld(i+nres),(vbldsc0(j,iti),
- c & AKSC(j,iti),abond0(j,iti),u(j),j=1,nbi)
+ if (lprn)
+ & write (iout,*) i,iti,vbld(i+nres),(vbldsc0(j,iti),
+ & AKSC(j,iti),abond0(j,iti),u(j),j=1,nbi)
estr=estr+uprod/usum
do j=1,3
gradbx(j,i)=usumsqder/(usum*usum)*dc(j,i+nres)/vbld(i+nres)
C Zero the energy function and its derivative at 0 or pi.
call splinthet(theta(i),0.5d0*delta,ss,ssd)
it=itype(i-1)
+ ichir1=isign(1,itype(i-2))
+ ichir2=isign(1,itype(i))
+ if (itype(i-2).eq.10) ichir1=isign(1,itype(i-1))
+ if (itype(i).eq.10) ichir2=isign(1,itype(i-1))
+ if (itype(i-1).eq.10) then
+ itype1=isign(10,itype(i-2))
+ ichir11=isign(1,itype(i-2))
+ ichir12=isign(1,itype(i-2))
+ itype2=isign(10,itype(i))
+ ichir21=isign(1,itype(i))
+ ichir22=isign(1,itype(i))
+ endif
c if (i.gt.ithet_start .and.
c & (itel(i-1).eq.0 .or. itel(i-2).eq.0)) goto 1215
c if (i.gt.3 .and. (i.le.4 .or. itel(i-3).ne.0)) then
C In following comments this theta will be referred to as t_c.
thet_pred_mean=0.0d0
do k=1,2
- athetk=athet(k,it)
- bthetk=bthet(k,it)
+ athetk=athet(k,it,ichir1,ichir2)
+ bthetk=bthet(k,it,ichir1,ichir2)
+ if (it.eq.10) then
+ athetk=athet(k,itype1,ichir11,ichir12)
+ bthetk=bthet(k,itype2,ichir21,ichir22)
+ endif
thet_pred_mean=thet_pred_mean+athetk*y(k)+bthetk*z(k)
enddo
c write (iout,*) "thet_pred_mean",thet_pred_mean
thet_pred_mean=thet_pred_mean*ss+a0thet(it)
c write (iout,*) "thet_pred_mean",thet_pred_mean
C Derivatives of the "mean" values in gamma1 and gamma2.
- dthetg1=(-athet(1,it)*y(2)+athet(2,it)*y(1))*ss
- dthetg2=(-bthet(1,it)*z(2)+bthet(2,it)*z(1))*ss
+ dthetg1=(-athet(1,it,ichir1,ichir2)*y(2)
+ &+athet(2,it,ichir1,ichir2)*y(1))*ss
+ dthetg2=(-bthet(1,it,ichir1,ichir2)*z(2)
+ & +bthet(2,it,ichir1,ichir2)*z(1))*ss
+ if (it.eq.10) then
+ dthetg1=(-athet(1,itype1,ichir11,ichir12)*y(2)
+ &+athet(2,itype1,ichir11,ichir12)*y(1))*ss
+ dthetg2=(-bthet(1,itype2,ichir21,ichir22)*z(2)
+ & +bthet(2,itype2,ichir21,ichir22)*z(1))*ss
+ endif
if (theta(i).gt.pi-delta) then
call theteng(pi-delta,thet_pred_mean,theta0(it),f0,fprim0,
& E_tc0)
etheta=0.0D0
c write (iout,*) "ithetyp",(ithetyp(i),i=1,ntyp1)
do i=ithet_start,ithet_end
+ if (iabs(itype(i+1)).eq.20) iblock=2
+ if (iabs(itype(i+1)).ne.20) iblock=1
dethetai=0.0d0
dephii=0.0d0
dephii1=0.0d0
theti2=0.5d0*theta(i)
- ityp2=ithetyp(itype(i-1))
+ ityp2=ithetyp((itype(i-1)))
do k=1,nntheterm
coskt(k)=dcos(k*theti2)
sinkt(k)=dsin(k*theti2)
#else
phii=phi(i)
#endif
- ityp1=ithetyp(itype(i-2))
+ ityp1=ithetyp(iabs(itype(i-2)))
do k=1,nsingle
cosph1(k)=dcos(k*phii)
sinph1(k)=dsin(k*phii)
#else
phii1=phi(i+1)
#endif
- ityp3=ithetyp(itype(i))
+ ityp3=ithetyp((itype(i)))
do k=1,nsingle
cosph2(k)=dcos(k*phii1)
sinph2(k)=dsin(k*phii1)
c write (iout,*) "i",i," ityp1",itype(i-2),ityp1,
c & " ityp2",itype(i-1),ityp2," ityp3",itype(i),ityp3
c call flush(iout)
- ethetai=aa0thet(ityp1,ityp2,ityp3)
+ ethetai=aa0thet(ityp1,ityp2,ityp3,iblock)
do k=1,ndouble
do l=1,k-1
ccl=cosph1(l)*cosph2(k-l)
enddo
endif
do k=1,ntheterm
- ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3)*sinkt(k)
- dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3)
+ ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3,iblock)*sinkt(k)
+ dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3,iblock)
& *coskt(k)
if (lprn)
- & write (iout,*) "k",k," aathet",aathet(k,ityp1,ityp2,ityp3),
+ & write (iout,*) "k",k," aathet",aathet(k,ityp1,ityp2,ityp3,
+ & iblock),
& " ethetai",ethetai
enddo
if (lprn) then
endif
do m=1,ntheterm2
do k=1,nsingle
- aux=bbthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)
- & +ccthet(k,m,ityp1,ityp2,ityp3)*sinph1(k)
- & +ddthet(k,m,ityp1,ityp2,ityp3)*cosph2(k)
- & +eethet(k,m,ityp1,ityp2,ityp3)*sinph2(k)
+ aux=bbthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k)
+ & +ccthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k)
+ & +ddthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k)
+ & +eethet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k)
ethetai=ethetai+sinkt(m)*aux
dethetai=dethetai+0.5d0*m*aux*coskt(m)
dephii=dephii+k*sinkt(m)*(
- & ccthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)-
- & bbthet(k,m,ityp1,ityp2,ityp3)*sinph1(k))
+ & ccthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k)-
+ & bbthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k))
dephii1=dephii1+k*sinkt(m)*(
- & eethet(k,m,ityp1,ityp2,ityp3)*cosph2(k)-
- & ddthet(k,m,ityp1,ityp2,ityp3)*sinph2(k))
+ & eethet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k)-
+ & ddthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k))
if (lprn)
& write (iout,*) "m",m," k",k," bbthet",
- & bbthet(k,m,ityp1,ityp2,ityp3)," ccthet",
- & ccthet(k,m,ityp1,ityp2,ityp3)," ddthet",
- & ddthet(k,m,ityp1,ityp2,ityp3)," eethet",
- & eethet(k,m,ityp1,ityp2,ityp3)," ethetai",ethetai
+ & bbthet(k,m,ityp1,ityp2,ityp3,iblock)," ccthet",
+ & ccthet(k,m,ityp1,ityp2,ityp3,iblock)," ddthet",
+ & ddthet(k,m,ityp1,ityp2,ityp3,iblock)," eethet",
+ & eethet(k,m,ityp1,ityp2,ityp3,iblock)," ethetai",ethetai
enddo
enddo
if (lprn)
do m=1,ntheterm3
do k=2,ndouble
do l=1,k-1
- aux=ffthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)
+ aux=ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)
ethetai=ethetai+sinkt(m)*aux
dethetai=dethetai+0.5d0*m*coskt(m)*aux
dephii=dephii+l*sinkt(m)*(
- & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)-
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+ & -ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)-
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l))
dephii1=dephii1+(k-l)*sinkt(m)*(
- & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)-
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+ & -ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)-
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l))
if (lprn) then
write (iout,*) "m",m," k",k," l",l," ffthet",
- & ffthet(l,k,m,ityp1,ityp2,ityp3),
- & ffthet(k,l,m,ityp1,ityp2,ityp3)," ggthet",
- & ggthet(l,k,m,ityp1,ityp2,ityp3),
- & ggthet(k,l,m,ityp1,ityp2,ityp3)," ethetai",ethetai
+ & ffthet(l,k,m,ityp1,ityp2,ityp3,iblock),
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)," ggthet",
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock),
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)," ethetai",
+ & ethetai
write (iout,*) cosph1ph2(l,k)*sinkt(m),
& cosph1ph2(k,l)*sinkt(m),
& sinph1ph2(l,k)*sinkt(m),sinph1ph2(k,l)*sinkt(m)
do i=loc_start,loc_end
it=itype(i)
if (it.eq.10) goto 1
- nlobit=nlob(it)
+ nlobit=nlob(iabs(it))
c print *,'i=',i,' it=',it,' nlobit=',nlobit
c write (iout,*) 'i=',i,' ssa=',ssa,' ssad=',ssad
theti=theta(i+1)-pipol
do iii=-1,1
do j=1,nlobit
- expfac=dexp(bsc(j,it)-0.5D0*contr(j,iii)+emin)
+ expfac=dexp(bsc(j,iabs(it))-0.5D0*contr(j,iii)+emin)
cd print *,'j=',j,' expfac=',expfac
escloc_i=escloc_i+expfac
do k=1,3
dersc12=0.0d0
do j=1,nlobit
- expfac=dexp(bsc(j,it)-0.5D0*contr(j)+emin)
+ expfac=dexp(bsc(j,iabs(it))-0.5D0*contr(j)+emin)
escloc_i=escloc_i+expfac
do k=1,2
dersc(k)=dersc(k)+Ax(k,j)*expfac
cosfac=dsqrt(cosfac2)
sinfac2=0.5d0/(1.0d0-costtab(i+1))
sinfac=dsqrt(sinfac2)
- it=itype(i)
+ it=iabs(itype(i))
if (it.eq.10) goto 1
c
C Compute the axes of tghe local cartesian coordinates system; store in
y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
enddo
do j = 1,3
- z_prime(j) = -uz(j,i-1)
+ z_prime(j) = -uz(j,i-1)*dsign(1.0d0,dfloat(itype(i)))
enddo
c write (2,*) "i",i
c write (2,*) "x_prime",(x_prime(j),j=1,3)
C Compute the energy of the ith side cbain
C
c write (2,*) "xx",xx," yy",yy," zz",zz
- it=itype(i)
+ it=iabs(itype(i))
do j = 1,65
x(j) = sc_parmin(j,it)
enddo
Cc diagnostics - remove later
xx1 = dcos(alph(2))
yy1 = dsin(alph(2))*dcos(omeg(2))
- zz1 = -dsin(alph(2))*dsin(omeg(2))
+ zz1 = -dsign(1.0d0,itype(i))*dsin(alph(2))*dsin(omeg(2))
write(2,'(3f8.1,3f9.3,1x,3f9.3)')
& alph(2)*rad2deg,omeg(2)*rad2deg,theta(3)*rad2deg,xx,yy,zz,
& xx1,yy1,zz1
escloc = escloc + sumene
c write (2,*) "escloc",escloc
if (.not. calc_grad) goto 1
- #ifdef DEBUG
+
+ #ifdef DEBUG2
C
C This section to check the numerical derivatives of the energy of ith side
C chain in xx, yy, zz, and theta. Use the -DDEBUG compiler option or insert
dZZ_Ci1(k)=0.0d0
dZZ_Ci(k)=0.0d0
do j=1,3
- dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)*dC_norm(j,i+nres)
- dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)*dC_norm(j,i+nres)
+ dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)
+ & *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres)
+ dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)
+ & *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres)
+
enddo
dXX_XYZ(k)=vbld_inv(i+nres)*(x_prime(k)-xx*dC_norm(k,i+nres))
etors=0.0D0
do i=iphi_start,iphi_end
if (itel(i-2).eq.0 .or. itel(i-1).eq.0) goto 1215
+ if (iabs(itype(i)).eq.20) then
+ iblock=2
+ else
+ iblock=1
+ endif
itori=itortyp(itype(i-2))
itori1=itortyp(itype(i-1))
phii=phi(i)
gloci=0.0D0
C Regular cosine and sine terms
- do j=1,nterm(itori,itori1)
- v1ij=v1(j,itori,itori1)
- v2ij=v2(j,itori,itori1)
+ do j=1,nterm(itori,itori1,iblock)
+ v1ij=v1(j,itori,itori1,iblock)
+ v2ij=v2(j,itori,itori1,iblock)
cosphi=dcos(j*phii)
sinphi=dsin(j*phii)
etors=etors+v1ij*cosphi+v2ij*sinphi
C
cosphi=dcos(0.5d0*phii)
sinphi=dsin(0.5d0*phii)
- do j=1,nlor(itori,itori1)
+ do j=1,nlor(itori,itori1,iblock)
vl1ij=vlor1(j,itori,itori1)
vl2ij=vlor2(j,itori,itori1)
vl3ij=vlor3(j,itori,itori1)
gloci=gloci+vl1ij*(vl3ij*cosphi-vl2ij*sinphi)*pom
enddo
C Subtract the constant term
- etors=etors-v0(itori,itori1)
+ etors=etors-v0(itori,itori1,iblock)
if (lprn)
& write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)')
& restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
- & (v1(j,itori,itori1),j=1,6),(v2(j,itori,itori1),j=1,6)
+ & (v1(j,itori,itori1,1),j=1,6),(v2(j,itori,itori1,1),j=1,6)
gloc(i-3,icg)=gloc(i-3,icg)+wtor*fact*gloci
c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg)
1215 continue
itori=itortyp(itype(i-2))
itori1=itortyp(itype(i-1))
itori2=itortyp(itype(i))
- c iblock=1
- c if (iabs(itype(i+1)).eq.20) iblock=2
phii=phi(i)
phii1=phi(i+1)
gloci1=0.0D0
gloci2=0.0D0
+ iblock=1
+ if (iabs(itype(i+1)).eq.20) iblock=2
C Regular cosine and sine terms
- do j=1,ntermd_1(itori,itori1,itori2)
- v1cij=v1c(1,j,itori,itori1,itori2)
- v1sij=v1s(1,j,itori,itori1,itori2)
- v2cij=v1c(2,j,itori,itori1,itori2)
- v2sij=v1s(2,j,itori,itori1,itori2)
+c c do j=1,ntermd_1(itori,itori1,itori2,iblock)
+c v1cij=v1c(1,j,itori,itori1,itori2,iblock)
+c v1sij=v1s(1,j,itori,itori1,itori2,iblock)
+c v2cij=v1c(2,j,itori,itori1,itori2,iblock)
+c v2sij=v1s(2,j,itori,itori1,itori2,iblock)
+ do j=1,ntermd_1(itori,itori1,itori2,iblock)
+ v1cij=v1c(1,j,itori,itori1,itori2,iblock)
+ v1sij=v1s(1,j,itori,itori1,itori2,iblock)
+ v2cij=v1c(2,j,itori,itori1,itori2,iblock)
+ v2sij=v1s(2,j,itori,itori1,itori2,iblock)
+
cosphi1=dcos(j*phii)
sinphi1=dsin(j*phii)
cosphi2=dcos(j*phii1)
gloci1=gloci1+j*(v1sij*cosphi1-v1cij*sinphi1)
gloci2=gloci2+j*(v2sij*cosphi2-v2cij*sinphi2)
enddo
- do k=2,ntermd_2(itori,itori1,itori2)
+ do k=2,ntermd_2(itori,itori1,itori2,iblock)
do l=1,k-1
- v1cdij = v2c(k,l,itori,itori1,itori2)
- v2cdij = v2c(l,k,itori,itori1,itori2)
- v1sdij = v2s(k,l,itori,itori1,itori2)
- v2sdij = v2s(l,k,itori,itori1,itori2)
+ v1cdij = v2c(k,l,itori,itori1,itori2,iblock)
+ v2cdij = v2c(l,k,itori,itori1,itori2,iblock)
+ v1sdij = v2s(k,l,itori,itori1,itori2,iblock)
+ v2sdij = v2s(l,k,itori,itori1,itori2,iblock)
cosphi1p2=dcos(l*phii+(k-l)*phii1)
cosphi1m2=dcos(l*phii-(k-l)*phii1)
sinphi1p2=dsin(l*phii+(k-l)*phii1)
C Set lprn=.true. for debugging
lprn=.false.
c lprn=.true.
- c write (iout,*) "EBACK_SC_COR",iphi_start,iphi_end,nterm_sccor
+ c write (iout,*) "EBACK_SC_COR",itau_start,itau_end,nterm_sccor
esccor=0.0D0
do i=itau_start,itau_end
esccor_ii=0.0D0
- isccori=isccortyp(itype(i-2))
- isccori1=isccortyp(itype(i-1))
+ isccori=isccortyp((itype(i-2)))
+ isccori1=isccortyp((itype(i-1)))
phii=phi(i)
cccc Added 9 May 2012
cc Tauangle is torsional engle depending on the value of first digit
c 3 = SC...Ca...Ca...SCi
gloci=0.0D0
if (((intertyp.eq.3).and.((itype(i-2).eq.10).or.
- & (itype(i-1).eq.10).or.(itype(i-2).eq.21).or.
- & (itype(i-1).eq.21)))
+ & (itype(i-1).eq.10).or.(itype(i-2).eq.ntyp1).or.
+ & (itype(i-1).eq.ntyp1)))
& .or. ((intertyp.eq.1).and.((itype(i-2).eq.10)
- & .or.(itype(i-2).eq.21)))
+ & .or.(itype(i-2).eq.ntyp1)))
& .or.((intertyp.eq.2).and.((itype(i-1).eq.10).or.
- & (itype(i-1).eq.21)))) cycle
- if ((intertyp.eq.2).and.(i.eq.4).and.(itype(1).eq.21)) cycle
- if ((intertyp.eq.1).and.(i.eq.nres).and.(itype(nres).eq.21))
+ & (itype(i-1).eq.ntyp1)))) cycle
+ if ((intertyp.eq.2).and.(i.eq.4).and.(itype(1).eq.ntyp1)) cycle
+ if ((intertyp.eq.1).and.(i.eq.nres).and.(itype(nres).eq.ntyp1))
& cycle
do j=1,nterm_sccor(isccori,isccori1)
v1ij=v1sccor(j,intertyp,isccori,isccori1)
& restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
& (v1sccor(j,intertyp,itori,itori1),j=1,6)
& ,(v2sccor(j,intertyp,itori,itori1),j=1,6)
- gsccor_loc(i-3)=gsccor_loc(i-3)+gloci
+c gsccor_loc(i-3)=gsccor_loc(i-3)+gloci
enddo !intertyp
enddo
c do i=1,nres
integer dimen1,dimen2,atom,indx
double precision buffer(dimen1,dimen2)
double precision zapas
- common /contacts_hb/ zapas(3,20,maxres,7),
- & facont_hb(20,maxres),ees0p(20,maxres),ees0m(20,maxres),
- & num_cont_hb(maxres),jcont_hb(20,maxres)
+ common /contacts_hb/ zapas(3,ntyp,maxres,7),
+ & facont_hb(ntyp,maxres),ees0p(ntyp,maxres),ees0m(ntyp,maxres),
+ & num_cont_hb(maxres),jcont_hb(ntyp,maxres)
num_kont=num_cont_hb(atom)
do i=1,num_kont
do k=1,7
integer dimen1,dimen2,atom,indx
double precision buffer(dimen1,dimen2)
double precision zapas
- common /contacts_hb/ zapas(3,20,maxres,7),
- & facont_hb(20,maxres),ees0p(20,maxres),ees0m(20,maxres),
- & num_cont_hb(maxres),jcont_hb(20,maxres)
+ common /contacts_hb/ zapas(3,ntyp,maxres,7),
+ & facont_hb(ntyp,maxres),ees0p(ntyp,maxres),
+ & ees0m(ntyp,maxres),
+ & num_cont_hb(maxres),jcont_hb(ntyp,maxres)
num_kont=buffer(1,indx+26)
num_kont_old=num_cont_hb(atom)
num_cont_hb(atom)=num_kont+num_kont_old
include 'COMMON.GEO'
logical swap
double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2),
- & auxvec1(2),auxvec2(1),auxmat1(2,2)
+ & auxvec1(2),auxvec2(2),auxmat1(2,2)
logical lprn
common /kutas/ lprn
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
igeom= 8
intin= 9
ithep= 11
+ ithep_pdb=51
irotam=12
+ irotam_pdb=52
itorp= 13
itordp= 23
ielep= 14
sigii(i)=0.0D0
rr0(i)=0.0D0
a0thet(i)=0.0D0
- do j=1,2
- athet(j,i)=0.0D0
- bthet(j,i)=0.0D0
+ do j=1,2
+ do ichir1=-1,1
+ do ichir2=-1,1
+ athet(j,i,ichir1,ichir2)=0.0D0
+ bthet(j,i,ichir1,ichir2)=0.0D0
+ enddo
+ enddo
enddo
do j=0,3
polthet(j,i)=0.0D0
enddo
nlob(ntyp1)=0
dsc(ntyp1)=0.0D0
- do i=1,maxtor
- itortyp(i)=0
- do j=1,maxtor
- do k=1,maxterm
- v1(k,j,i)=0.0D0
- v2(k,j,i)=0.0D0
+ do i=-maxtor,maxtor
+ itortyp(i)=0
+ do iblock=1,2
+ do j=-maxtor,maxtor
+ do k=1,maxterm
+ v1(k,j,i,iblock)=0.0D0
+ v2(k,j,i,iblock)=0.0D0
enddo
enddo
+ enddo
enddo
+ do iblock=1,2
+ do i=-maxtor,maxtor
+ do j=-maxtor,maxtor
+ do k=-maxtor,maxtor
+ do l=1,maxtermd_1
+ v1c(1,l,i,j,k,iblock)=0.0D0
+ v1s(1,l,i,j,k,iblock)=0.0D0
+ v1c(2,l,i,j,k,iblock)=0.0D0
+ v1s(2,l,i,j,k,iblock)=0.0D0
+ enddo !l
+ do l=1,maxtermd_2
+ do m=1,maxtermd_2
+ v2c(m,l,i,j,k,iblock)=0.0D0
+ v2s(m,l,i,j,k,iblock)=0.0D0
+ enddo !m
+ enddo !l
+ enddo !k
+ enddo !j
+ enddo !i
+ enddo !iblock
do i=1,maxres
itype(i)=0
itel(i)=0
ihpb(i)=0
jhpb(i)=0
enddo
+ do i=1,maxres
+ dyn_ss_mask(i)=.false.
+ enddo
C
C Initialize timing.
C
include 'COMMON.WEIGHTS'
include 'COMMON.FFIELD'
data restyp /
+ &'DD' ,'DPR','DLY','DAR','DHI','DAS','DGL','DSG','DGN','DSN','DTH',
+ &'DYY','DAL','DTY','DTR','DVA','DLE','DIL','DPN','MED','DCY','ZER',
&'CYS','MET','PHE','ILE','LEU','VAL','TRP','TYR','ALA','GLY','THR',
&'SER','GLN','ASN','GLU','ASP','HIS','ARG','LYS','PRO','D'/
data onelet /
+ &'z','p','k','r','h','d','e','n','q','s','t','g',
+ &'a','y','w','v','l','i','f','m','c','x',
&'C','M','F','I','L','V','W','Y','A','G','T',
&'S','Q','N','E','D','H','R','K','P','X'/
data potname /'LJ','LJK','BP','GB','GBV'/
cd & (ihpb(i),jhpb(i),i=1,nss)
do i=nnt,nct-1
scheck=.false.
+ if (dyn_ss) go to 10
do ii=1,nss
if (ihpb(ii).eq.i+nres) then
scheck=.true.
nint_gr(i)=1
istart(i,1)=i+1
iend(i,1)=nct
- ind_scint=int_scint+nct-i
+ ind_scint=ind_scint+nct-i
#endif
endif
#ifdef MPL
endif
enddo ! i
#endif
- if (lprint) then
+ if (lprint) then
write (iout,'(a)') 'SC-p interaction array:'
do i=iatscp_s,iatscp_e
write (iout,'(i3,2(2x,2i3))')
write (iout,'(20i4)') (itype(i),i=1,nres)
do i=1,nres-1
#ifdef PROCOR
- if (itype(i).eq.21 .or. itype(i+1).eq.21) then
+ if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) then
#else
- if (itype(i).eq.21) then
+ if (itype(i).eq.ntyp1) then
#endif
itel(i)=0
#ifdef PROCOR
- else if (itype(i+1).ne.20) then
+ else if (iabs(itype(i+1)).ne.20) then
#else
- else if (itype(i).ne.20) then
+ else if (iabs(itype(i)).ne.20) then
#endif
itel(i)=1
else
nnt=1
nct=nres
- if (itype(1).eq.21) nnt=2
- if (itype(nres).eq.21) nct=nct-1
+ if (itype(1).eq.ntyp1) nnt=2
+ if (itype(nres).eq.ntyp1) nct=nct-1
write(iout,*) 'NNT=',NNT,' NCT=',NCT
c Read distance restraints
if (constr_dist.gt.0) then
+ if (refstr) call read_ref_structure(*11)
call read_dist_constr
call hpb_partition
endif
endif
write (iout,'(a)')
return
+ 11 stop "Error reading reference structure"
end
c-----------------------------------------------------------------------------
logical function seq_comp(itypea,itypeb,length)
enddo
endif
endif
+ if (ns.gt.0.and.dyn_ss) then
+ C /06/28/2013 Adasko:ns is number of Cysteins bonded also called half of
+ C the bond
+ do i=nss+1,nhpb
+ C /06/28/2013 Adasko: nss number of full SS bonds
+ ihpb(i-nss)=ihpb(i)
+ jhpb(i-nss)=jhpb(i)
+ forcon(i-nss)=forcon(i)
+ dhpb(i-nss)=dhpb(i)
+ enddo
+ nhpb=nhpb-nss
+ nss=0
+ call hpb_partition
+ do i=1,ns
+ dyn_ss_mask(iss(i))=.true.
+ C /06/28/2013 Adasko: dyn_ss_mask which Cysteins can form disulfidebond
+ c write(iout,*) i,iss(i),dyn_ss_mask(iss(i)),"ATU"
+ enddo
+ endif
return
end
c------------------------------------------------------------------------------
include 'COMMON.FREE'
character*1 t1,t2,t3
character*1 onelett(4) /"G","A","P","D"/
- character*1 toronelet(-2:2)/"p","a","G","A","P"/
logical lprint
dimension blower(3,3,maxlob)
character*800 controlcard
key = wname(i)(:ilen(wname(i)))
call reada(controlcard,key(:ilen(key)),ww(i),1.0d0)
enddo
-
+ call reada(controlcard,"D0CM",d0cm,3.78d0)
+ call reada(controlcard,"AKCM",akcm,15.1d0)
+ call reada(controlcard,"AKTH",akth,11.0d0)
+ call reada(controlcard,"AKCT",akct,12.0d0)
+ call reada(controlcard,"V1SS",v1ss,-1.08d0)
+ call reada(controlcard,"V2SS",v2ss,7.61d0)
+ call reada(controlcard,"V3SS",v3ss,13.7d0)
+ call reada(controlcard,"EBR",ebr,-5.50D0)
+ c dyn_ss=(index(controlcard,'DYN_SS').gt.0)
write (iout,*) "iparm",iparm," myparm",myparm
- c If reading not own parameters, skip assignment
+ c do i=1,maxres
+ c dyn_ss_mask(i)=.false.
+ c enddo
+ do i=1,maxres-1
+ do j=i+1,maxres
+ dyn_ssbond_ij(i,j)=1.0d300
+ enddo
+ enddo
+ call reada(controlcard,"HT",Ht,0.0D0)
+ c if(me.eq.king.or..not.out1file) then
+ c print *,'indpdb=',indpdb,' pdbref=',pdbref
+ c endif
+ c If reading not own parameters, skip assignment
+ cc write(iout,*) "KURWA", ww(15)
if (iparm.eq.myparm .or. .not.separate_parset) then
c
wtor=ww(13)
wtor_d=ww(14)
wvdwpp=ww(16)
+ wstrain=ww(15)
wbond=ww(18)
wsccor=ww(19)
endif
+ cc write(iout,*) "KURWA", wstrain,akcm,akth,wsc,dyn_ss
call card_concat(controlcard,.false.)
call reads(controlcard,"TORDPAR",tordname_t,tordname)
open (itordp,file=tordname_t,status='old')
rewind(itordp)
- call reads(controlcard,"SCCORAR",sccorname_t,sccorname)
+ call reads(controlcard,"SCCORPAR",sccorname_t,sccorname)
open (isccor,file=sccorname_t,status='old')
rewind(isccor)
call reads(controlcard,"FOURIER",fouriername_t,fouriername)
C of the virtual-bond valence angles theta
C
do i=1,ntyp
- read (ithep,*) a0thet(i),(athet(j,i),j=1,2),(bthet(j,i),j=1,2)
+ read (ithep,*) a0thet(i),(athet(j,i,1,1),j=1,2),
+ & (bthet(j,i,1,1),j=1,2)
read (ithep,*) (polthet(j,i),j=0,3)
read (ithep,*) (gthet(j,i),j=1,3)
read (ithep,*) theta0(i),sig0(i),sigc0(i)
sigc0(i)=sigc0(i)**2
enddo
+ do i=1,ntyp
+ athet(1,i,1,-1)=athet(1,i,1,1)
+ athet(2,i,1,-1)=athet(2,i,1,1)
+ bthet(1,i,1,-1)=-bthet(1,i,1,1)
+ bthet(2,i,1,-1)=-bthet(2,i,1,1)
+ athet(1,i,-1,1)=-athet(1,i,1,1)
+ athet(2,i,-1,1)=-athet(2,i,1,1)
+ bthet(1,i,-1,1)=bthet(1,i,1,1)
+ bthet(2,i,-1,1)=bthet(2,i,1,1)
+ enddo
+ do i=-ntyp,-1
+ a0thet(i)=a0thet(-i)
+ athet(1,i,-1,-1)=athet(1,-i,1,1)
+ athet(2,i,-1,-1)=-athet(2,-i,1,1)
+ bthet(1,i,-1,-1)=bthet(1,-i,1,1)
+ bthet(2,i,-1,-1)=-bthet(2,-i,1,1)
+ athet(1,i,-1,1)=athet(1,-i,1,1)
+ athet(2,i,-1,1)=-athet(2,-i,1,1)
+ bthet(1,i,-1,1)=-bthet(1,-i,1,1)
+ bthet(2,i,-1,1)=bthet(2,-i,1,1)
+ athet(1,i,1,-1)=-athet(1,-i,1,1)
+ athet(2,i,1,-1)=athet(2,-i,1,1)
+ bthet(1,i,1,-1)=bthet(1,-i,1,1)
+ bthet(2,i,1,-1)=-bthet(2,-i,1,1)
+ theta0(i)=theta0(-i)
+ sig0(i)=sig0(-i)
+ sigc0(i)=sigc0(-i)
+ do j=0,3
+ polthet(j,i)=polthet(j,-i)
+ enddo
+ do j=1,3
+ gthet(j,i)=gthet(j,-i)
+ enddo
+ enddo
close (ithep)
if (lprint) then
c write (iout,'(a)')
& ' b1*10^1 ',' b2*10^1 '
do i=1,ntyp
write(iout,'(a3,1h&,2x,5(f8.3,1h&))') restyp(i),
- & a0thet(i),(100*athet(j,i),j=1,2),(10*bthet(j,i),j=1,2)
+ & a0thet(i),(100*athet(j,i,1,1),j=1,2),
+ & (10*bthet(j,i,1,1),j=1,2)
enddo
write (iout,'(/a/9x,5a/79(1h-))')
& 'Parameters of the expression for sigma(theta_c):',
& ntheterm3,nsingle,ndouble
nntheterm=max0(ntheterm,ntheterm2,ntheterm3)
read (ithep,*) (ithetyp(i),i=1,ntyp1)
- do i=1,maxthetyp
- do j=1,maxthetyp
- do k=1,maxthetyp
- aa0thet(i,j,k)=0.0d0
+ do i=-ntyp1,-1
+ ithetyp(i)=-ithetyp(-i)
+ enddo
+c write (iout,*) "tu dochodze"
+ do iblock=1,2
+ do i=-maxthetyp,maxthetyp
+ do j=-maxthetyp,maxthetyp
+ do k=-maxthetyp,maxthetyp
+ aa0thet(i,j,k,iblock)=0.0d0
do l=1,ntheterm
- aathet(l,i,j,k)=0.0d0
+ aathet(l,i,j,k,iblock)=0.0d0
enddo
do l=1,ntheterm2
do m=1,nsingle
- bbthet(m,l,i,j,k)=0.0d0
- ccthet(m,l,i,j,k)=0.0d0
- ddthet(m,l,i,j,k)=0.0d0
- eethet(m,l,i,j,k)=0.0d0
+ bbthet(m,l,i,j,k,iblock)=0.0d0
+ ccthet(m,l,i,j,k,iblock)=0.0d0
+ ddthet(m,l,i,j,k,iblock)=0.0d0
+ eethet(m,l,i,j,k,iblock)=0.0d0
enddo
enddo
do l=1,ntheterm3
do m=1,ndouble
do mm=1,ndouble
- ffthet(mm,m,l,i,j,k)=0.0d0
- ggthet(mm,m,l,i,j,k)=0.0d0
+ ffthet(mm,m,l,i,j,k,iblock)=0.0d0
+ ggthet(mm,m,l,i,j,k,iblock)=0.0d0
enddo
enddo
enddo
enddo
enddo
+ enddo
enddo
- do i=1,nthetyp
- do j=1,nthetyp
- do k=1,nthetyp
- read (ithep,'(3a)') res1,res2,res3
- read (ithep,*) aa0thet(i,j,k)
- read (ithep,*)(aathet(l,i,j,k),l=1,ntheterm)
+
+ do iblock=1,2
+ do i=0,nthetyp
+ do j=-nthetyp,nthetyp
+ do k=-nthetyp,nthetyp
+ read (ithep,'(6a)') res1
+ read (ithep,*) aa0thet(i,j,k,iblock)
+ read (ithep,*)(aathet(l,i,j,k,iblock),l=1,ntheterm)
read (ithep,*)
- & ((bbthet(lll,ll,i,j,k),lll=1,nsingle),
- & (ccthet(lll,ll,i,j,k),lll=1,nsingle),
- & (ddthet(lll,ll,i,j,k),lll=1,nsingle),
- & (eethet(lll,ll,i,j,k),lll=1,nsingle),ll=1,ntheterm2)
+ & ((bbthet(lll,ll,i,j,k,iblock),lll=1,nsingle),
+ & (ccthet(lll,ll,i,j,k,iblock),lll=1,nsingle),
+ & (ddthet(lll,ll,i,j,k,iblock),lll=1,nsingle),
+ & (eethet(lll,ll,i,j,k,iblock),lll=1,nsingle)
+ & ,ll=1,ntheterm2)
read (ithep,*)
- & (((ffthet(llll,lll,ll,i,j,k),ffthet(lll,llll,ll,i,j,k),
- & ggthet(llll,lll,ll,i,j,k),ggthet(lll,llll,ll,i,j,k),
+ & (((ffthet(llll,lll,ll,i,j,k,iblock),
+ & ffthet(lll,llll,ll,i,j,k,iblock),
+ & ggthet(llll,lll,ll,i,j,k,iblock)
+ & ,ggthet(lll,llll,ll,i,j,k,iblock),
& llll=1,lll-1),lll=2,ndouble),ll=1,ntheterm3)
enddo
enddo
do i=1,nthetyp
do j=1,nthetyp
do l=1,ntheterm
- aathet(l,i,j,nthetyp+1)=aathet(l,i,j,1)
- aathet(l,nthetyp+1,i,j)=aathet(l,1,i,j)
+ aathet(l,i,j,nthetyp+1,iblock)=0.0d0
+ aathet(l,nthetyp+1,i,j,iblock)=0.0d0
enddo
- aa0thet(i,j,nthetyp+1)=aa0thet(i,j,1)
- aa0thet(nthetyp+1,i,j)=aa0thet(1,i,j)
+ aa0thet(i,j,nthetyp+1,iblock)=0.0d0
+ aa0thet(nthetyp+1,i,j,iblock)=0.0d0
enddo
do l=1,ntheterm
- aathet(l,nthetyp+1,i,nthetyp+1)=aathet(l,1,i,1)
+ aathet(l,nthetyp+1,i,nthetyp+1,iblock)=0.0d0
enddo
- aa0thet(nthetyp+1,i,nthetyp+1)=aa0thet(1,i,1)
+ aa0thet(nthetyp+1,i,nthetyp+1,iblock)=0.0d0
enddo
+ enddo
+C Substitution for D aminoacids from symmetry.
+ do iblock=1,2
+ do i=-nthetyp,0
+ do j=-nthetyp,nthetyp
+ do k=-nthetyp,nthetyp
+ aa0thet(i,j,k,iblock)=aa0thet(-i,-j,-k,iblock)
+ do l=1,ntheterm
+ aathet(l,i,j,k,iblock)=aathet(l,-i,-j,-k,iblock)
+ enddo
+ do ll=1,ntheterm2
+ do lll=1,nsingle
+ bbthet(lll,ll,i,j,k,iblock)=bbthet(lll,ll,-i,-j,-k,iblock)
+ ccthet(lll,ll,i,j,k,iblock)=-ccthet(lll,ll,-i,-j,-k,iblock)
+ ddthet(lll,ll,i,j,k,iblock)=ddthet(lll,ll,-i,-j,-k,iblock)
+ eethet(lll,ll,i,j,k,iblock)=-eethet(lll,ll,-i,-j,-k,iblock)
+ enddo
+ enddo
+ do ll=1,ntheterm3
+ do lll=2,ndouble
+ do llll=1,lll-1
+ ffthet(llll,lll,ll,i,j,k,iblock)=
+ & ffthet(llll,lll,ll,-i,-j,-k,iblock)
+ ffthet(lll,llll,ll,i,j,k,iblock)=
+ & ffthet(lll,llll,ll,-i,-j,-k,iblock)
+ ggthet(llll,lll,ll,i,j,k,iblock)=
+ & -ggthet(llll,lll,ll,-i,-j,-k,iblock)
+ ggthet(lll,llll,ll,i,j,k,iblock)=
+ & -ggthet(lll,llll,ll,-i,-j,-k,iblock)
+ enddo !ll
+ enddo !lll
+ enddo !llll
+ enddo !k
+ enddo !j
+ enddo !i
+ enddo !iblock
C
C Control printout of the coefficients of virtual-bond-angle potentials
C
write (iout,'(//4a)')
& 'Type ',onelett(i),onelett(j),onelett(k)
write (iout,'(//a,10x,a)') " l","a[l]"
- write (iout,'(i2,1pe15.5)') 0,aa0thet(i,j,k)
+ write (iout,'(i2,1pe15.5)') 0,aa0thet(i,j,k,iblock)
write (iout,'(i2,1pe15.5)')
- & (l,aathet(l,i,j,k),l=1,ntheterm)
+ & (l,aathet(l,i,j,k,iblock),l=1,ntheterm)
do l=1,ntheterm2
write (iout,'(//2h m,4(9x,a,3h[m,i1,1h]))')
& "b",l,"c",l,"d",l,"e",l
do m=1,nsingle
write (iout,'(i2,4(1pe15.5))') m,
- & bbthet(m,l,i,j,k),ccthet(m,l,i,j,k),
- & ddthet(m,l,i,j,k),eethet(m,l,i,j,k)
+ & bbthet(m,l,i,j,k,iblock),ccthet(m,l,i,j,k,iblock),
+ & ddthet(m,l,i,j,k,iblock),eethet(m,l,i,j,k,iblock)
enddo
enddo
do l=1,ntheterm3
do m=2,ndouble
do n=1,m-1
write (iout,'(i1,1x,i1,4(1pe15.5))') n,m,
- & ffthet(n,m,l,i,j,k),ffthet(m,n,l,i,j,k),
- & ggthet(n,m,l,i,j,k),ggthet(m,n,l,i,j,k)
+ & ffthet(n,m,l,i,j,k,iblock),
+ & ffthet(m,n,l,i,j,k,iblock),
+ & ggthet(n,m,l,i,j,k,iblock),
+ & ggthet(m,n,l,i,j,k,iblock)
enddo
enddo
enddo
enddo
bsc(1,i)=0.0D0
read(irotam,*)(censc(k,1,i),k=1,3),((blower(k,l,1),l=1,k),k=1,3)
+ censc(1,1,-i)=censc(1,1,i)
+ censc(2,1,-i)=censc(2,1,i)
+ censc(3,1,-i)=-censc(3,1,i)
do j=2,nlob(i)
read (irotam,*) bsc(j,i)
read (irotam,*) (censc(k,j,i),k=1,3),
& ((blower(k,l,j),l=1,k),k=1,3)
+ censc(1,j,-i)=censc(1,j,i)
+ censc(2,j,-i)=censc(2,j,i)
+ censc(3,j,-i)=-censc(3,j,i)
enddo
do j=1,nlob(i)
do k=1,3
enddo
gaussc(k,l,j,i)=akl
gaussc(l,k,j,i)=akl
+ if (((k.eq.3).and.(l.ne.3))
+ & .or.((l.eq.3).and.(k.ne.3))) then
+ gaussc(k,l,j,-i)=-akl
+ gaussc(l,k,j,-i)=-akl
+ else
+ gaussc(k,l,j,-i)=akl
+ gaussc(l,k,j,-i)=akl
+ endif
enddo
enddo
enddo
C
read (itorp,*) ntortyp
read (itorp,*) (itortyp(i),i=1,ntyp)
- write (iout,*) 'ntortyp',ntortyp
- do i=1,ntortyp
- do j=1,ntortyp
- read (itorp,*) nterm(i,j),nlor(i,j)
+ do iblock=1,2
+ do i=-ntyp,-1
+ itortyp(i)=-itortyp(-i)
+ enddo
+c write (iout,*) 'ntortyp',ntortyp
+ do i=0,ntortyp-1
+ do j=-ntortyp+1,ntortyp-1
+ read (itorp,*) nterm(i,j,iblock),
+ & nlor(i,j,iblock)
+ nterm(-i,-j,iblock)=nterm(i,j,iblock)
+ nlor(-i,-j,iblock)=nlor(i,j,iblock)
v0ij=0.0d0
si=-1.0d0
- do k=1,nterm(i,j)
- read (itorp,*) kk,v1(k,i,j),v2(k,i,j)
- v0ij=v0ij+si*v1(k,i,j)
+ do k=1,nterm(i,j,iblock)
+ read (itorp,*) kk,v1(k,i,j,iblock),v2(k,i,j,iblock)
+ v1(k,-i,-j,iblock)=v1(k,i,j,iblock)
+ v2(k,-i,-j,iblock)=-v2(k,i,j,iblock)
+ v0ij=v0ij+si*v1(k,i,j,iblock)
si=-si
enddo
- do k=1,nlor(i,j)
+ do k=1,nlor(i,j,iblock)
read (itorp,*) kk,vlor1(k,i,j),vlor2(k,i,j),vlor3(k,i,j)
v0ij=v0ij+vlor1(k,i,j)/(1+vlor3(k,i,j)**2)
enddo
- v0(i,j)=v0ij
+ v0(i,j,iblock)=v0ij
+ v0(-i,-j,iblock)=v0ij
enddo
enddo
+ enddo
close (itorp)
if (lprint) then
write (iout,'(/a/)') 'Torsional constants:'
do j=1,ntortyp
write (iout,*) 'ityp',i,' jtyp',j
write (iout,*) 'Fourier constants'
- do k=1,nterm(i,j)
- write (iout,'(2(1pe15.5))') v1(k,i,j),v2(k,i,j)
+ do k=1,nterm(i,j,iblock)
+ write (iout,'(2(1pe15.5))') v1(k,i,j,iblock),
+ & v2(k,i,j,iblock)
enddo
write (iout,*) 'Lorenz constants'
- do k=1,nlor(i,j)
+ do k=1,nlor(i,j,iblock)
write (iout,'(3(1pe15.5))')
& vlor1(k,i,j),vlor2(k,i,j),vlor3(k,i,j)
enddo
C
C 6/23/01 Read parameters for double torsionals
C
- do i=1,ntortyp
- do j=1,ntortyp
- do k=1,ntortyp
+ do iblock=1,2
+ do i=0,ntortyp-1
+ do j=-ntortyp+1,ntortyp-1
+ do k=-ntortyp+1,ntortyp-1
read (itordp,'(3a1)') t1,t2,t3
- if (t1.ne.toronelet(i) .or. t2.ne.toronelet(j)
- & .or. t3.ne.toronelet(k)) then
+ if (t1.ne.onelett(i) .or. t2.ne.onelett(j)
+ & .or. t3.ne.onelett(k)) then
write (iout,*) "Error in double torsional parameter file",
& i,j,k,t1,t2,t3
stop "Error in double torsional parameter file"
endif
- read (itordp,*) ntermd_1(i,j,k),ntermd_2(i,j,k)
- read (itordp,*) (v1c(1,l,i,j,k),l=1,ntermd_1(i,j,k))
- read (itordp,*) (v1s(1,l,i,j,k),l=1,ntermd_1(i,j,k))
- read (itordp,*) (v1c(2,l,i,j,k),l=1,ntermd_1(i,j,k))
- read (itordp,*) (v1s(2,l,i,j,k),l=1,ntermd_1(i,j,k))
- read (itordp,*) ((v2c(l,m,i,j,k),v2c(m,l,i,j,k),
- & v2s(l,m,i,j,k),v2s(m,l,i,j,k),m=1,l-1),l=1,ntermd_2(i,j,k))
- enddo
- enddo
- enddo
+ read (itordp,*) ntermd_1(i,j,k,iblock),
+ & ntermd_2(i,j,k,iblock)
+ ntermd_1(-i,-j,-k,iblock)=ntermd_1(i,j,k,iblock)
+ ntermd_2(-i,-j,-k,iblock)=ntermd_2(i,j,k,iblock)
+ read (itordp,*) (v1c(1,l,i,j,k,iblock),l=1,
+ & ntermd_1(i,j,k,iblock))
+ read (itordp,*) (v1s(1,l,i,j,k,iblock),l=1,
+ & ntermd_1(i,j,k,iblock))
+ read (itordp,*) (v1c(2,l,i,j,k,iblock),l=1,
+ & ntermd_1(i,j,k,iblock))
+ read (itordp,*) (v1s(2,l,i,j,k,iblock),l=1,
+ & ntermd_1(i,j,k,iblock))
+C Martix of D parameters for one dimesional foureir series
+ do l=1,ntermd_1(i,j,k,iblock)
+ v1c(1,l,-i,-j,-k,iblock)=v1c(1,l,i,j,k,iblock)
+ v1s(1,l,-i,-j,-k,iblock)=-v1s(1,l,i,j,k,iblock)
+ v1c(2,l,-i,-j,-k,iblock)=v1c(2,l,i,j,k,iblock)
+ v1s(2,l,-i,-j,-k,iblock)=-v1s(2,l,i,j,k,iblock)
+c write(iout,*) "whcodze" ,
+c & v1s(2,l,-i,-j,-k,iblock),v1s(2,l,i,j,k,iblock)
+ enddo
+ read (itordp,*) ((v2c(l,m,i,j,k,iblock),
+ & v2c(m,l,i,j,k,iblock),v2s(l,m,i,j,k,iblock),
+ & v2s(m,l,i,j,k,iblock),
+ & m=1,l-1),l=1,ntermd_2(i,j,k,iblock))
+C Martix of D parameters for two dimesional fourier series
+ do l=1,ntermd_2(i,j,k,iblock)
+ do m=1,l-1
+ v2c(l,m,-i,-j,-k,iblock)=v2c(l,m,i,j,k,iblock)
+ v2c(m,l,-i,-j,-k,iblock)=v2c(m,l,i,j,k,iblock)
+ v2s(l,m,-i,-j,-k,iblock)=-v2s(l,m,i,j,k,iblock)
+ v2s(m,l,-i,-j,-k,iblock)=-v2s(m,l,i,j,k,iblock)
+ enddo!m
+ enddo!l
+ enddo!k
+ enddo!j
+ enddo!i
+ enddo!iblock
if (lprint) then
write (iout,*)
write (iout,*) 'Constants for double torsionals'
- do i=1,ntortyp
- do j=1,ntortyp
- do k=1,ntortyp
+ do iblock=1,2
+ do i=0,ntortyp-1
+ do j=-ntortyp+1,ntortyp-1
+ do k=-ntortyp+1,ntortyp-1
write (iout,*) 'ityp',i,' jtyp',j,' ktyp',k,
- & ' nsingle',ntermd_1(i,j,k),' ndouble',ntermd_2(i,j,k)
+ & ' nsingle',ntermd_1(i,j,k,iblock),
+ & ' ndouble',ntermd_2(i,j,k,iblock)
write (iout,*)
write (iout,*) 'Single angles:'
- do l=1,ntermd_1(i,j,k)
+ do l=1,ntermd_1(i,j,k,iblock)
write (iout,'(i5,2f10.5,5x,2f10.5)') l,
- & v1c(1,l,i,j,k),v1s(1,l,i,j,k),
- & v1c(2,l,i,j,k),v1s(2,l,i,j,k)
+ & v1c(1,l,i,j,k,iblock),v1s(1,l,i,j,k,iblock),
+ & v1c(2,l,i,j,k,iblock),v1s(2,l,i,j,k,iblock)
enddo
write (iout,*)
write (iout,*) 'Pairs of angles:'
- write (iout,'(3x,20i10)') (l,l=1,ntermd_2(i,j,k))
- do l=1,ntermd_2(i,j,k)
+ write (iout,'(3x,20i10)') (l,l=1,ntermd_2(i,j,k,iblock))
+ do l=1,ntermd_2(i,j,k,iblock)
write (iout,'(i5,20f10.5)')
- & l,(v2c(l,m,i,j,k),m=1,ntermd_2(i,j,k))
+ & l,(v2c(l,m,i,j,k,iblock),m=1,ntermd_2(i,j,k,iblock))
enddo
write (iout,*)
- write (iout,'(3x,20i10)') (l,l=1,ntermd_2(i,j,k))
- do l=1,ntermd_2(i,j,k)
+ write (iout,'(3x,20i10)') (l,l=1,ntermd_2(i,j,k,iblock))
+ do l=1,ntermd_2(i,j,k,iblock)
write (iout,'(i5,20f10.5)')
- & l,(v2s(l,m,i,j,k),m=1,ntermd_2(i,j,k))
+ & l,(v2s(l,m,i,j,k,iblock),m=1,ntermd_2(i,j,k,iblock))
enddo
write (iout,*)
enddo
enddo
enddo
+ enddo
endif
#endif
C Read of Side-chain backbone correlation parameters
C
read (isccor,*) nsccortyp
read (isccor,*) (isccortyp(i),i=1,ntyp)
+ do i=-ntyp,-1
+ isccortyp(i)=-isccortyp(-i)
+ enddo
+ iscprol=isccortyp(20)
c write (iout,*) 'ntortyp',ntortyp
maxinter=3
cc maxinter is maximum interaction sites
do j=1,nsccortyp
read (isccor,*) nterm_sccor(i,j),nlor_sccor(i,j)
v0ijsccor=0.0d0
+ v0ijsccor1=0.0d0
+ v0ijsccor2=0.0d0
+ v0ijsccor3=0.0d0
si=-1.0d0
-
+ nterm_sccor(-i,j)=nterm_sccor(i,j)
+ nterm_sccor(-i,-j)=nterm_sccor(i,j)
+ nterm_sccor(i,-j)=nterm_sccor(i,j)
do k=1,nterm_sccor(i,j)
read (isccor,*) kk,v1sccor(k,l,i,j)
& ,v2sccor(k,l,i,j)
+ if (j.eq.iscprol) then
+ if (i.eq.isccortyp(10)) then
+ v1sccor(k,l,i,-j)=v1sccor(k,l,i,j)
+ v2sccor(k,l,i,-j)=-v2sccor(k,l,i,j)
+ else
+ v1sccor(k,l,i,-j)=v1sccor(k,l,i,j)*0.5d0
+ & +v2sccor(k,l,i,j)*dsqrt(0.75d0)
+ v2sccor(k,l,i,-j)=-v2sccor(k,l,i,j)*0.5d0
+ & +v1sccor(k,l,i,j)*dsqrt(0.75d0)
+ v1sccor(k,l,-i,-j)=v1sccor(k,l,i,j)
+ v2sccor(k,l,-i,-j)=-v2sccor(k,l,i,j)
+ v1sccor(k,l,-i,j)=v1sccor(k,l,i,-j)
+ v2sccor(k,l,-i,j)=-v2sccor(k,l,i,-j)
+ endif
+ else
+ if (i.eq.isccortyp(10)) then
+ v1sccor(k,l,i,-j)=v1sccor(k,l,i,j)
+ v2sccor(k,l,i,-j)=-v2sccor(k,l,i,j)
+ else
+ if (j.eq.isccortyp(10)) then
+ v1sccor(k,l,-i,j)=v1sccor(k,l,i,j)
+ v2sccor(k,l,-i,j)=-v2sccor(k,l,i,j)
+ else
+ v1sccor(k,l,i,-j)=-v1sccor(k,l,i,j)
+ v2sccor(k,l,i,-j)=-v2sccor(k,l,i,j)
+ v1sccor(k,l,-i,-j)=v1sccor(k,l,i,j)
+ v2sccor(k,l,-i,-j)=-v2sccor(k,l,i,j)
+ v1sccor(k,l,-i,j)=v1sccor(k,l,i,-j)
+ v2sccor(k,l,-i,j)=-v2sccor(k,l,i,-j)
+ endif
+ endif
+ endif
v0ijsccor=v0ijsccor+si*v1sccor(k,l,i,j)
+ v0ijsccor1=v0ijsccor+si*v1sccor(k,l,-i,j)
+ v0ijsccor2=v0ijsccor+si*v1sccor(k,l,i,-j)
+ v0ijsccor3=v0ijsccor+si*v1sccor(k,l,-i,-j)
si=-si
enddo
do k=1,nlor_sccor(i,j)
v0ijsccor=v0ijsccor+vlor1sccor(k,i,j)/
&(1+vlor3sccor(k,i,j)**2)
enddo
- v0sccor(i,j)=v0ijsccor
+ v0sccor(l,i,j)=v0ijsccor
+ v0sccor(l,-i,j)=v0ijsccor1
+ v0sccor(l,i,-j)=v0ijsccor2
+ v0sccor(l,-i,-j)=v0ijsccor3
enddo
enddo
enddo
C interaction energy of the Gly, Ala, and Pro prototypes.
C
read (ifourier,*) nloctyp
- do i=1,nloctyp
+ do i=0,nloctyp-1
read (ifourier,*)
- read (ifourier,*) (b(ii,i),ii=1,13)
+ read (ifourier,*) (b(ii),ii=1,13)
if (lprint) then
write (iout,*) 'Type',i
- write (iout,'(a,i2,a,f10.5)') ('b(',ii,')=',b(ii,i),ii=1,13)
+ write (iout,'(a,i2,a,f10.5)') ('b(',ii,')=',b(ii),ii=1,13)
endif
- B1(1,i) = b(3,i)
- B1(2,i) = b(5,i)
- B1tilde(1,i) = b(3,i)
- B1tilde(2,i) =-b(5,i)
- B2(1,i) = b(2,i)
- B2(2,i) = b(4,i)
- CC(1,1,i)= b(7,i)
- CC(2,2,i)=-b(7,i)
- CC(2,1,i)= b(9,i)
- CC(1,2,i)= b(9,i)
- Ctilde(1,1,i)=b(7,i)
- Ctilde(1,2,i)=b(9,i)
- Ctilde(2,1,i)=-b(9,i)
- Ctilde(2,2,i)=b(7,i)
- DD(1,1,i)= b(6,i)
- DD(2,2,i)=-b(6,i)
- DD(2,1,i)= b(8,i)
- DD(1,2,i)= b(8,i)
- Dtilde(1,1,i)=b(6,i)
- Dtilde(1,2,i)=b(8,i)
- Dtilde(2,1,i)=-b(8,i)
- Dtilde(2,2,i)=b(6,i)
- EE(1,1,i)= b(10,i)+b(11,i)
- EE(2,2,i)=-b(10,i)+b(11,i)
- EE(2,1,i)= b(12,i)-b(13,i)
- EE(1,2,i)= b(12,i)+b(13,i)
+ B1(1,i) = b(3)
+ B1(2,i) = b(5)
+ B1(1,-i) = b(3)
+ B1(2,-i) = -b(5)
+c b1(1,i)=0.0d0
+c b1(2,i)=0.0d0
+ B1tilde(1,i) = b(3)
+ B1tilde(2,i) =-b(5)
+ B1tilde(1,-i) =-b(3)
+ B1tilde(2,-i) =b(5)
+c b1tilde(1,i)=0.0d0
+c b1tilde(2,i)=0.0d0
+ B2(1,i) = b(2)
+ B2(2,i) = b(4)
+ B2(1,-i) =b(2)
+ B2(2,-i) =-b(4)
+
+c b2(1,i)=0.0d0
+c b2(2,i)=0.0d0
+ CC(1,1,i)= b(7)
+ CC(2,2,i)=-b(7)
+ CC(2,1,i)= b(9)
+ CC(1,2,i)= b(9)
+ CC(1,1,-i)= b(7)
+ CC(2,2,-i)=-b(7)
+ CC(2,1,-i)=-b(9)
+ CC(1,2,-i)=-b(9)
+c CC(1,1,i)=0.0d0
+c CC(2,2,i)=0.0d0
+c CC(2,1,i)=0.0d0
+c CC(1,2,i)=0.0d0
+ Ctilde(1,1,i)=b(7)
+ Ctilde(1,2,i)=b(9)
+ Ctilde(2,1,i)=-b(9)
+ Ctilde(2,2,i)=b(7)
+ Ctilde(1,1,-i)=b(7)
+ Ctilde(1,2,-i)=-b(9)
+ Ctilde(2,1,-i)=b(9)
+ Ctilde(2,2,-i)=b(7)
+
+c Ctilde(1,1,i)=0.0d0
+c Ctilde(1,2,i)=0.0d0
+c Ctilde(2,1,i)=0.0d0
+c Ctilde(2,2,i)=0.0d0
+ DD(1,1,i)= b(6)
+ DD(2,2,i)=-b(6)
+ DD(2,1,i)= b(8)
+ DD(1,2,i)= b(8)
+ DD(1,1,-i)= b(6)
+ DD(2,2,-i)=-b(6)
+ DD(2,1,-i)=-b(8)
+ DD(1,2,-i)=-b(8)
+c DD(1,1,i)=0.0d0
+c DD(2,2,i)=0.0d0
+c DD(2,1,i)=0.0d0
+c DD(1,2,i)=0.0d0
+ Dtilde(1,1,i)=b(6)
+ Dtilde(1,2,i)=b(8)
+ Dtilde(2,1,i)=-b(8)
+ Dtilde(2,2,i)=b(6)
+ Dtilde(1,1,-i)=b(6)
+ Dtilde(1,2,-i)=-b(8)
+ Dtilde(2,1,-i)=b(8)
+ Dtilde(2,2,-i)=b(6)
+
+c Dtilde(1,1,i)=0.0d0
+c Dtilde(1,2,i)=0.0d0
+c Dtilde(2,1,i)=0.0d0
+c Dtilde(2,2,i)=0.0d0
+ EE(1,1,i)= b(10)+b(11)
+ EE(2,2,i)=-b(10)+b(11)
+ EE(2,1,i)= b(12)-b(13)
+ EE(1,2,i)= b(12)+b(13)
+ EE(1,1,-i)= b(10)+b(11)
+ EE(2,2,-i)=-b(10)+b(11)
+ EE(2,1,-i)=-b(12)+b(13)
+ EE(1,2,-i)=-b(12)-b(13)
+
+c ee(1,1,i)=1.0d0
+c ee(2,2,i)=1.0d0
+c ee(2,1,i)=0.0d0
+c ee(1,2,i)=0.0d0
+c ee(2,1,i)=ee(1,2,i)
enddo
if (lprint) then
do i=1,nloctyp
enddo
enddo
C
- C Define the SC-p interaction constants
+ C Define the SC-p interaction constants and SS bond potentials
C
+ if (dyn_ss) then
+ ss_depth=ebr/wsc-0.25*eps(1,1)
+ Ht=Ht/wsc-0.25*eps(1,1)
+ akcm=akcm*wstrain/wsc
+ akth=akth*wstrain/wsc
+ akct=akct*wstrain/wsc
+ v1ss=v1ss*wstrain/wsc
+ v2ss=v2ss*wstrain/wsc
+ v3ss=v3ss*wstrain/wsc
+ else
+ ss_depth=ebr/wstrain-0.25*eps(1,1)*wsc/wstrain
+ endif
+ write (iout,*) "Parameters of the SS-bond potential:"
+ write (iout,*) "D0CM",d0cm," AKCM",akcm," AKTH",akth,
+ & " AKCT",akct
+ write (iout,*) "V1SS",v1ss," V2SS",v2ss," V3SS",v3ss
+ write (iout,*) "EBR",ebr," SS_DEPTH",ss_depth
+ write (iout,*)" HT",Ht
+
#ifdef OLDSCP
do i=1,20
C "Soft" SC-p repulsion (causes helices to be too flat, but facilitates
C
C Define the constants of the disulfide bridge
C
- ebr=-5.50D0
+ c ebr=-5.50D0
c
c Old arbitrary potential - commented out.
c
c energy surface of diethyl disulfide.
c A. Liwo and U. Kozlowska, 11/24/03
c
- D0CM = 3.78d0
- AKCM = 15.1d0
- AKTH = 11.0d0
- AKCT = 12.0d0
- V1SS =-1.08d0
- V2SS = 7.61d0
- V3SS = 13.7d0
+ c D0CM = 3.78d0
+ c AKCM = 15.1d0
+ c AKTH = 11.0d0
+ c AKCT = 12.0d0
+ c V1SS =-1.08d0
+ c V2SS = 7.61d0
+ c V3SS = 13.7d0
- if (lprint) then
- write (iout,'(/a)') "Disulfide bridge parameters:"
- write (iout,'(a,f10.2)') 'S-S bridge energy: ',ebr
- write (iout,'(2(a,f10.2))') 'd0cm:',d0cm,' akcm:',akcm
- write (iout,'(2(a,f10.2))') 'akth:',akth,' akct:',akct
- write (iout,'(3(a,f10.2))') 'v1ss:',v1ss,' v2ss:',v2ss,
- & ' v3ss:',v3ss
- endif
+ c if (lprint) then
+ c write (iout,'(/a)') "Disulfide bridge parameters:"
+ c write (iout,'(a,f10.2)') 'S-S bridge energy: ',ebr
+ c write (iout,'(2(a,f10.2))') 'd0cm:',d0cm,' akcm:',akcm
+ c write (iout,'(2(a,f10.2))') 'akth:',akth,' akct:',akct
+ c write (iout,'(3(a,f10.2))') 'v1ss:',v1ss,' v2ss:',v2ss,
+ c & ' v3ss:',v3ss
+ c endif
return
end
include 'COMMON.SCROT'
include 'COMMON.SCCOR'
include 'COMMON.ALLPARM'
- integer i,j,k,l,m,mm,iparm
+ integer i,j,k,l,m,mm,iparm,ichir1,ichir2,iblock,iii
c Store weights
ww_all(1,iparm)=wsc
enddo
c Store bond angle parameters
#ifdef CRYST_THETA
- do i=1,ntyp
+ do i=-ntyp,ntyp
a0thet_all(i,iparm)=a0thet(i)
+ do ichir1=-1,1
+ do ichir2=-1,1
do j=1,2
- athet_all(j,i,iparm)=athet(j,i)
- bthet_all(j,i,iparm)=bthet(j,i)
+ athet_all(j,i,ichir1,ichir2,iparm)=athet(j,i,ichir1,ichir2)
+ bthet_all(j,i,ichir1,ichir2,iparm)=bthet(j,i,ichir1,ichir2)
+ enddo
+ enddo
enddo
do j=0,3
polthet_all(j,i,iparm)=polthet(j,i)
#endif
#ifdef CRYST_SC
c Store the sidechain rotamer parameters
- do i=1,ntyp
- nlob_all(i,iparm)=nlob(i)
- do j=1,nlob(i)
- bsc_all(j,i,iparm)=bsc(j,i)
+ do i=-ntyp,ntyp
+ iii=iabs(i)
+ if (i.eq.0) cycle
+ nlob_all(iii,iparm)=nlob(iii)
+ do j=1,nlob(iii)
+ bsc_all(j,iii,iparm)=bsc(j,iii)
do k=1,3
censc_all(k,j,i,iparm)=censc(k,j,i)
enddo
enddo
#endif
c Store the torsional parameters
- do i=1,ntortyp
- do j=1,ntortyp
- v0_all(i,j,iparm)=v0(i,j)
- nterm_all(i,j,iparm)=nterm(i,j)
- nlor_all(i,j,iparm)=nlor(i,j)
- do k=1,nterm(i,j)
- v1_all(k,i,j,iparm)=v1(k,i,j)
- v2_all(k,i,j,iparm)=v2(i,i,j)
- enddo
- do k=1,nlor(i,j)
- vlor1_all(k,i,j,iparm)=vlor1(k,i,j)
- vlor2_all(k,i,j,iparm)=vlor2(k,i,j)
- vlor3_all(k,i,j,iparm)=vlor3(k,i,j)
- enddo
- enddo
- enddo
+ do iblock=1,2
+ do i=-ntortyp+1,ntortyp-1
+ do j=-ntortyp+1,ntortyp-1
+ v0_all(i,j,iblock,iparm)=v0(i,j,iblock)
+ nterm_all(i,j,iblock,iparm)=nterm(i,j,iblock)
+ nlor_all(i,j,iblock,iparm)=nlor(i,j,iblock)
+ do k=1,nterm(i,j,iblock)
+ v1_all(k,i,j,iblock,iparm)=v1(k,i,j,iblock)
+ v2_all(k,i,j,iblock,iparm)=v2(k,i,j,iblock)
+ enddo
+ do k=1,nlor(i,j,iblock)
+ vlor1_all(k,i,j,iparm)=vlor1(k,i,j)
+ vlor2_all(k,i,j,iparm)=vlor2(k,i,j)
+ vlor3_all(k,i,j,iparm)=vlor3(k,i,j)
+ enddo
+ enddo
+ enddo
+ enddo
c Store the double torsional parameters
- do i=1,ntortyp
- do j=1,ntortyp
- do k=1,ntortyp
- ntermd1_all(i,j,k,iparm)=ntermd_1(i,j,k)
- ntermd2_all(i,j,k,iparm)=ntermd_2(i,j,k)
- do l=1,ntermd_1(i,j,k)
- v1c_all(1,l,i,j,k,iparm)=v1c(1,l,i,j,k)
- v1c_all(2,l,i,j,k,iparm)=v1c(2,l,i,j,k)
- v2c_all(1,l,i,j,k,iparm)=v2c(1,l,i,j,k)
- v2c_all(2,l,i,j,k,iparm)=v2c(2,l,i,j,k)
- enddo
- do l=1,ntermd_2(i,j,k)
- do m=1,ntermd_2(i,j,k)
- v2s_all(l,m,i,j,k,iparm)=v2s(l,m,i,j,k)
- enddo
- enddo
- enddo
- enddo
+ do iblock=1,2
+ do i=-ntortyp+1,ntortyp-1
+ do j=-ntortyp+1,ntortyp-1
+ do k=-ntortyp+1,ntortyp-1
+ ntermd1_all(i,j,k,iblock,iparm)=ntermd_1(i,j,k,iblock)
+ ntermd2_all(i,j,k,iblock,iparm)=ntermd_2(i,j,k,iblock)
+ do l=1,ntermd_1(i,j,k,iblock)
+ v1c_all(1,l,i,j,k,iblock,iparm)=v1c(1,l,i,j,k,iblock)
+ v1c_all(2,l,i,j,k,iblock,iparm)=v1c(2,l,i,j,k,iblock)
+ v2c_all(1,l,i,j,k,iblock,iparm)=v2c(1,l,i,j,k,iblock)
+ v2c_all(2,l,i,j,k,iblock,iparm)=v2c(2,l,i,j,k,iblock)
+ enddo
+ do l=1,ntermd_2(i,j,k,iblock)
+ do m=1,ntermd_2(i,j,k,iblock)
+ v2s_all(l,m,i,j,k,iblock,iparm)=v2s(l,m,i,j,k,iblock)
+ enddo
+ enddo
+ enddo
+ enddo
+ enddo
enddo
c Store parameters of the cumulants
- do i=1,nloctyp
+ do i=-nloctyp,nloctyp
do j=1,2
b1_all(j,i,iparm)=b1(j,i)
b1tilde_all(j,i,iparm)=b1tilde(j,i)
enddo
enddo
c Store disulfide-bond parameters
+ ht_all(iparm)=ht
+ ss_depth_all(iparm)=ss_depth
ebr_all(iparm)=ebr
d0cm_all(iparm)=d0cm
akcm_all(iparm)=akcm
include 'COMMON.SCROT'
include 'COMMON.SCCOR'
include 'COMMON.ALLPARM'
- integer i,j,k,l,m,mm,iparm
+ integer i,j,k,l,m,mm,iparm,ichir1,ichir2,iblock,iii
c Restore weights
wsc=ww_all(1,iparm)
enddo
c Restore bond angle parameters
#ifdef CRYST_THETA
- do i=1,ntyp
+ do i=-ntyp,ntyp
a0thet(i)=a0thet_all(i,iparm)
+
+ do ichir1=-1,1
+ do ichir2=-1,1
do j=1,2
- athet(j,i)=athet_all(j,i,iparm)
- bthet(j,i)=bthet_all(j,i,iparm)
- enddo
+ athet(j,i,ichir1,ichir2)=athet_all(j,i,ichir1,ichir2,iparm)
+ bthet(j,i,ichir1,ichir2)=bthet_all(j,i,ichir1,ichir2,iparm)
+ enddo
+ enddo
+ enddo
do j=0,3
polthet(j,i)=polthet_all(j,i,iparm)
enddo
#endif
c Restore the sidechain rotamer parameters
#ifdef CRYST_SC
- do i=1,ntyp
- nlob(i)=nlob_all(i,iparm)
- do j=1,nlob(i)
- bsc(j,i)=bsc_all(j,i,iparm)
+ do i=-ntyp,ntyp
+ if (i.eq.0) cycle
+ iii=iabs(i)
+ nlob(iii)=nlob_all(iii,iparm)
+ do j=1,nlob(iii)
+ bsc(j,iii)=bsc_all(j,iii,iparm)
do k=1,3
censc(k,j,i)=censc_all(k,j,i,iparm)
enddo
enddo
#endif
c Restore the torsional parameters
- do i=1,ntortyp
- do j=1,ntortyp
- v0(i,j)=v0_all(i,j,iparm)
- nterm(i,j)=nterm_all(i,j,iparm)
- nlor(i,j)=nlor_all(i,j,iparm)
- do k=1,nterm(i,j)
- v1(k,i,j)=v1_all(k,i,j,iparm)
- v2(i,i,j)=v2_all(k,i,j,iparm)
- enddo
- do k=1,nlor(i,j)
- vlor1(k,i,j)=vlor1_all(k,i,j,iparm)
- vlor2(k,i,j)=vlor2_all(k,i,j,iparm)
- vlor3(k,i,j)=vlor3_all(k,i,j,iparm)
- enddo
- enddo
- enddo
+ do iblock=1,2
+ do i=-ntortyp+1,ntortyp-1
+ do j=-ntortyp+1,ntortyp-1
+ v0(i,j,iblock)=v0_all(i,j,iblock,iparm)
+ nterm(i,j,iblock)=nterm_all(i,j,iblock,iparm)
+ nlor(i,j,iblock)=nlor_all(i,j,iblock,iparm)
+ do k=1,nterm(i,j,iblock)
+ v1(k,i,j,iblock)=v1_all(k,i,j,iblock,iparm)
+ v2(k,i,j,iblock)=v2_all(k,i,j,iblock,iparm)
+ enddo
+ do k=1,nlor(i,j,iblock)
+ vlor1(k,i,j)=vlor1_all(k,i,j,iparm)
+ vlor2(k,i,j)=vlor2_all(k,i,j,iparm)
+ vlor3(k,i,j)=vlor3_all(k,i,j,iparm)
+ enddo
+ enddo
+ enddo
+ enddo
c Restore the double torsional parameters
- do i=1,ntortyp
- do j=1,ntortyp
- do k=1,ntortyp
- ntermd_1(i,j,k)=ntermd1_all(i,j,k,iparm)
- ntermd_2(i,j,k)=ntermd2_all(i,j,k,iparm)
- do l=1,ntermd_1(i,j,k)
- v1c(1,l,i,j,k)=v1c_all(1,l,i,j,k,iparm)
- v1c(2,l,i,j,k)=v1c_all(2,l,i,j,k,iparm)
- v2c(1,l,i,j,k)=v2c_all(1,l,i,j,k,iparm)
- v2c(2,l,i,j,k)=v2c_all(2,l,i,j,k,iparm)
- enddo
- do l=1,ntermd_2(i,j,k)
- do m=1,ntermd_2(i,j,k)
- v2s(l,m,i,j,k)=v2s_all(l,m,i,j,k,iparm)
- enddo
- enddo
- enddo
- enddo
+ do iblock=1,2
+ do i=-ntortyp+1,ntortyp-1
+ do j=-ntortyp+1,ntortyp-1
+ do k=-ntortyp+1,ntortyp-1
+ ntermd_1(i,j,k,iblock)=ntermd1_all(i,j,k,iblock,iparm)
+ ntermd_2(i,j,k,iblock)=ntermd2_all(i,j,k,iblock,iparm)
+ do l=1,ntermd_1(i,j,k,iblock)
+ v1c(1,l,i,j,k,iblock)=v1c_all(1,l,i,j,k,iblock,iparm)
+ v1c(2,l,i,j,k,iblock)=v1c_all(2,l,i,j,k,iblock,iparm)
+ v2c(1,l,i,j,k,iblock)=v2c_all(1,l,i,j,k,iblock,iparm)
+ v2c(2,l,i,j,k,iblock)=v2c_all(2,l,i,j,k,iblock,iparm)
+ enddo
+ do l=1,ntermd_2(i,j,k,iblock)
+ do m=1,ntermd_2(i,j,k,iblock)
+ v2s(l,m,i,j,k,iblock)=v2s_all(l,m,i,j,k,iblock,iparm)
+ enddo
+ enddo
+ enddo
+ enddo
+ enddo
enddo
c Restore parameters of the cumulants
- do i=1,nloctyp
+ do i=-nloctyp,nloctyp
do j=1,2
b1(j,i)=b1_all(j,i,iparm)
b1tilde(j,i)=b1tilde_all(j,i,iparm)
enddo
enddo
c Restore disulfide-bond parameters
+ ht=ht_all(iparm)
+ ss_depth=ss_depth_all(iparm)
ebr=ebr_all(iparm)
d0cm=d0cm_all(iparm)
akcm=akcm_all(iparm)
projects / unres.git / commitdiff