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)
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'
+C triple bond artifac removal
+ do k=j+1,iend(i,iint)
+C search over all next residues
+ if (dyn_ss_mask(k)) then
+C check if they are cysteins
+C write(iout,*) 'k=',k
+ call triple_ssbond_ene(i,j,k,evdwij)
+C call the energy function that removes the artifical triple disulfide
+C bond the soubroutine is located in ssMD.F
+ evdw=evdw+evdwij
+ if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)')
+ & 'evdw',i,j,evdwij,'tss'
+ endif!dyn_ss_mask(k)
+ enddo! k
+ ELSE
+C cycle
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))
+ 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
+ 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) 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,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
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)
+ dthetg2=(-bthet(1,it,ichir1,ichir2)*z(2)
& +bthet(2,it,ichir1,ichir2)*z(1))*ss
- if (it.eq.10) then
+ 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
+ endif
if (theta(i).gt.pi-delta) then
call theteng(pi-delta,thet_pred_mean,theta0(it),f0,fprim0,
& E_tc0)
enddo
enddo
10 continue
- if (lprn1) write (iout,'(i2,3f8.1,9h ethetai ,f10.5)')
- & i,theta(i)*rad2deg,phii*rad2deg,
+c lprn1=.true.
+ if (lprn1) write (iout,'(a4,i2,3f8.1,9h ethetai ,f10.5)')
+ & 'ebe', 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
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
c lprn=.true.
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
+ 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))
- if (iabs(itype(i)).eq.20) then
- iblock=2
- else
- iblock=1
- endif
phii=phi(i)
gloci=0.0D0
C Regular cosine and sine terms
lprn=.false.
c lprn=.true.
etors_d=0.0D0
+c write(iout,*) "a tu??"
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
+ 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))
- iblock=1
- 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,iblock)
v1cij=v1c(1,j,itori,itori1,itori2,iblock)
v1sij=v1s(1,j,itori,itori1,itori2,iblock)
enddo
gloc(i-3,icg)=gloc(i-3,icg)+wtor_d*gloci1
gloc(i-2,icg)=gloc(i-2,icg)+wtor_d*gloci2
-c write (iout,*) "gloci", gloc(i-3,icg)
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