! write (iout,100)
! do i=1,nres
-! write (iout,110) restyp(itype(i)),i,c(1,i),c(2,i),&
+! write (iout,110) restyp(itype(i,1)),i,c(1,i),c(2,i),&
! c(3,i),c(1,nres+i),c(2,nres+i),c(3,nres+i)
! enddo
! 100 format (//' alpha-carbon coordinates ',&
! read secondary structure prediction from JPRED here!
! read(isecpred,'(A80)',err=100,end=100) line
! read(line,'(f10.3)',err=110) ftors
- read(isecpred,'(f10.3)',err=110) ftors
+ read(isecpred,'(f10.3)',err=110) ftors(1)
- write (iout,*) 'FTORS factor =',ftors
+ write (iout,*) 'FTORS factor =',ftors(1)
! initialize secstruc to any
do i=1,nres
secstruc(i) ='-'
ii=0
do i=1,nres
+ ftors(i)=ftors(1)
if ( secstruc(i) .eq. 'H') then
! Helix restraints for this residue
ii=ii+1
use geometry_data
use energy_data
- use control_data, only:maxtor,maxterm
+ use control_data, only:maxterm !,maxtor
use MD_data
use MPI_data
!el use map_data
character(len=1) :: toronelet(-2:2) = (/"p","a","G","A","P"/)
logical :: lprint,LaTeX
real(kind=8),dimension(3,3,maxlob) :: blower !(3,3,maxlob)
- real(kind=8),dimension(13) :: b
+ real(kind=8),dimension(13) :: buse
character(len=3) :: lancuch !,ucase
!el local variables
integer :: m,n,l,i,j,k,iblock,lll,llll,ll,nlobi,mm
- integer :: maxinter,junk,kk,ii
+ integer :: maxinter,junk,kk,ii,ncatprotparm
real(kind=8) :: v0ijsccor,v0ijsccor1,v0ijsccor2,v0ijsccor3,si,&
dwa16,rjunk,akl,v0ij,rri,epsij,rrij,sigeps,sigt1sq,&
sigt2sq,sigii1,sigii2,ratsig1,ratsig2,rsum_max,r_augm,&
- res1
+ res1,epsijlip,epspeptube,epssctube,sigmapeptube, &
+ sigmasctube
integer :: ichir1,ichir2
! real(kind=8),dimension(maxterm,-maxtor:maxtor,-maxtor:maxtor,2) :: v1_el,v2_el !(maxterm,-maxtor:maxtor,-maxtor:maxtor,2)
!el allocate(v1_el(maxterm,-maxtor:maxtor,-maxtor:maxtor,2))
!
allocate(dsc(ntyp1)) !(ntyp1)
allocate(dsc_inv(ntyp1)) !(ntyp1)
+ allocate(nbondterm_nucl(ntyp_molec(2))) !(ntyp)
+ allocate(vbldsc0_nucl(maxbondterm,ntyp_molec(2))) !(maxbondterm,ntyp)
+ allocate(aksc_nucl(maxbondterm,ntyp_molec(2))) !(maxbondterm,ntyp)
allocate(nbondterm(ntyp)) !(ntyp)
allocate(vbldsc0(maxbondterm,ntyp)) !(maxbondterm,ntyp)
allocate(aksc(maxbondterm,ntyp)) !(maxbondterm,ntyp)
- allocate(msc(ntyp+1)) !(ntyp+1)
- allocate(isc(ntyp+1)) !(ntyp+1)
- allocate(restok(ntyp+1)) !(ntyp+1)
allocate(abond0(maxbondterm,ntyp)) !(maxbondterm,ntyp)
-
+ allocate(long_r_sidechain(ntyp))
+ allocate(short_r_sidechain(ntyp))
dsc(:)=0.0d0
dsc_inv(:)=0.0d0
#ifdef CRYST_BOND
+ allocate(msc(ntyp+1)) !(ntyp+1)
+ allocate(isc(ntyp+1)) !(ntyp+1)
+ allocate(restok(ntyp+1)) !(ntyp+1)
+
read (ibond,*) vbldp0,akp,mp,ip,pstok
do i=1,ntyp
nbondterm(i)=1
endif
enddo
#else
- read (ibond,*) junk,vbldp0,akp,rjunk,mp,ip,pstok
- do i=1,ntyp
+ mp(:)=0.0d0
+ ip(:)=0.0d0
+ msc(:,:)=0.0d0
+ isc(:,:)=0.0d0
+
+ allocate(msc(ntyp+1,5)) !(ntyp+1)
+ allocate(isc(ntyp+1,5)) !(ntyp+1)
+ allocate(restok(ntyp+1,5)) !(ntyp+1)
+
+ read (ibond,*) junk,vbldp0,vbldpDUM,akp,rjunk,mp(1),ip(1),pstok(1)
+ do i=1,ntyp_molec(1)
read (ibond,*) nbondterm(i),(vbldsc0(j,i),aksc(j,i),abond0(j,i),&
- j=1,nbondterm(i)),msc(i),isc(i),restok(i)
+ j=1,nbondterm(i)),msc(i,1),isc(i,1),restok(i,1)
dsc(i) = vbldsc0(1,i)
if (i.eq.10) then
dsc_inv(i)=0.0D0
endif
enddo
#endif
+ read (ibond_nucl,*) vbldp0_nucl,akp_nucl,mp(2),ip(2),pstok(2)
+ do i=1,ntyp_molec(2)
+ nbondterm_nucl(i)=1
+ read (ibond_nucl,*) vbldsc0_nucl(1,i),aksc_nucl(1,i),msc(i,2),isc(i,2),restok(i,2)
+! dsc(i) = vbldsc0_nucl(1,i)
+! if (i.eq.10) then
+! dsc_inv(i)=0.0D0
+! else
+! dsc_inv(i)=1.0D0/dsc(i)
+! endif
+ enddo
+! read (ibond_nucl,*) junk,vbldp0_nucl,akp_nucl,rjunk,mp(2),ip(2),pstok(2)
+! do i=1,ntyp_molec(2)
+! read (ibond_nucl,*) nbondterm_nucl(i),(vbldsc0_nucl(j,i),&
+! aksc_nucl(j,i),abond0_nucl(j,i),&
+! j=1,nbondterm_nucl(i)),msc(i,2),isc(i,2),restok(i,2)
+! dsc(i) = vbldsc0(1,i)
+! if (i.eq.10) then
+! dsc_inv(i)=0.0D0
+! else
+! dsc_inv(i)=1.0D0/dsc(i)
+! endif
+! enddo
+
if (lprint) then
write(iout,'(/a/)')"Dynamic constants of the interaction sites:"
write (iout,'(a10,a3,6a10)') 'Type','N','VBL','K','A0','mass',&
'inertia','Pstok'
- write(iout,'(a10,i3,6f10.5)') "p",1,vbldp0,akp,0.0d0,mp,ip,pstok
+ write(iout,'(a10,i3,6f10.5)') "p",1,vbldp0,akp,0.0d0,mp(1),ip(1),pstok(1)
do i=1,ntyp
- write (iout,'(a10,i3,6f10.5)') restyp(i),nbondterm(i),&
- vbldsc0(1,i),aksc(1,i),abond0(1,i),msc(i),isc(i),restok(i)
+ write (iout,'(a10,i3,6f10.5)') restyp(i,1),nbondterm(i),&
+ vbldsc0(1,i),aksc(1,i),abond0(1,i),msc(i,1),isc(i,1),restok(i,1)
do j=2,nbondterm(i)
write (iout,'(13x,3f10.5)') &
vbldsc0(j,i),aksc(j,i),abond0(j,i)
enddo
enddo
endif
+ do i=1,ntyp_molec(5)
+ read(iion,*) msc(i,5),restok(i,5)
+ print *,msc(i,5),restok(i,5)
+ enddo
+ ip(5)=0.2
+! isc(5)=0.2
+ read (iion,*) ncatprotparm
+ allocate(catprm(ncatprotparm,4))
+ do k=1,4
+ read (iion,*) (catprm(i,k),i=1,ncatprotparm)
+ enddo
+ print *, catprm
+! read (iion,*) (vcatprm(k),k=1,ncatprotpram)
!----------------------------------------------------
allocate(a0thet(-ntyp:ntyp),theta0(-ntyp:ntyp))
allocate(sig0(-ntyp:ntyp),sigc0(-ntyp:ntyp)) !(-ntyp:ntyp)
theta0(:)=0.0D0
sig0(:)=0.0D0
sigc0(:)=0.0D0
+ allocate(liptranene(ntyp))
+!C reading lipid parameters
+ write (iout,*) "iliptranpar",iliptranpar
+ call flush(iout)
+ read(iliptranpar,*) pepliptran
+ print *,pepliptran
+ do i=1,ntyp
+ read(iliptranpar,*) liptranene(i)
+ print *,liptranene(i)
+ enddo
+ close(iliptranpar)
#ifdef CRYST_THETA
!
' ATHETA0 ',' A1 ',' A2 ',&
' B1 ',' B2 '
do i=1,ntyp
- write(iout,'(a3,i4,2x,5(1pe14.5))') restyp(i),i,&
+ write(iout,'(a3,i4,2x,5(1pe14.5))') restyp(i,1),i,&
a0thet(i),(athet(j,i,1,1),j=1,2),(bthet(j,i,1,1),j=1,2)
enddo
write (iout,'(/a/9x,5a/79(1h-))') &
' ALPH0 ',' ALPH1 ',' ALPH2 ',&
' ALPH3 ',' SIGMA0C '
do i=1,ntyp
- write (iout,'(a3,i4,2x,5(1pe14.5))') restyp(i),i,&
+ write (iout,'(a3,i4,2x,5(1pe14.5))') restyp(i,1),i,&
(polthet(j,i),j=0,3),sigc0(i)
enddo
write (iout,'(/a/9x,5a/79(1h-))') &
' THETA0 ',' SIGMA0 ',' G1 ',&
' G2 ',' G3 '
do i=1,ntyp
- write (iout,'(a3,i4,2x,5(1pe14.5))') restyp(i),i,theta0(i),&
+ write (iout,'(a3,i4,2x,5(1pe14.5))') restyp(i,1),i,theta0(i),&
sig0(i),(gthet(j,i),j=1,3)
enddo
else
' theta0 ',' a1*10^2 ',' a2*10^2 ',&
' b1*10^1 ',' b2*10^1 '
do i=1,ntyp
- write(iout,'(a3,1h&,2x,5(f8.3,1h&))') restyp(i),&
+ write(iout,'(a3,1h&,2x,5(f8.3,1h&))') restyp(i,1),&
a0thet(i),(100*athet(j,i,1,1),j=1,2),&
(10*bthet(j,i,1,1),j=1,2)
enddo
' alpha0 ',' alph1 ',' alph2 ',&
' alhp3 ',' sigma0c '
do i=1,ntyp
- write (iout,'(a3,1h&,2x,5(1pe12.3,1h&))') restyp(i),&
+ write (iout,'(a3,1h&,2x,5(1pe12.3,1h&))') restyp(i,1),&
(polthet(j,i),j=0,3),sigc0(i)
enddo
write (iout,'(/a/9x,5a/79(1h-))') &
' theta0 ',' sigma0*10^2 ',' G1*10^-1',&
' G2 ',' G3*10^1 '
do i=1,ntyp
- write (iout,'(a3,1h&,2x,5(f8.3,1h&))') restyp(i),theta0(i),&
+ write (iout,'(a3,1h&,2x,5(f8.3,1h&))') restyp(i,1),theta0(i),&
100*sig0(i),gthet(1,i)*0.1D0,gthet(2,i),gthet(3,i)*10.0D0
enddo
endif
!----------------------------------------------------
allocate(ithetyp(-ntyp1:ntyp1)) !(-ntyp1:ntyp1)
- allocate(aa0thet(-maxthetyp1:maxthetyp1,&
- -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
+ allocate(aa0thet(-nthetyp-1:nthetyp+1,&
+ -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
!(-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
- allocate(aathet(ntheterm,-maxthetyp1:maxthetyp1,&
- -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
+ allocate(aathet(ntheterm,-nthetyp-1:nthetyp+1,&
+ -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
!(maxtheterm,-maxthetyp1:maxthetyp1,&
! -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
- allocate(bbthet(nsingle,ntheterm2,-maxthetyp1:maxthetyp1,&
- -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
- allocate(ccthet(nsingle,ntheterm2,-maxthetyp1:maxthetyp1,&
- -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
- allocate(ddthet(nsingle,ntheterm2,-maxthetyp1:maxthetyp1,&
- -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
- allocate(eethet(nsingle,ntheterm2,-maxthetyp1:maxthetyp1,&
- -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
+ allocate(bbthet(nsingle,ntheterm2,-nthetyp-1:nthetyp+1,&
+ -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
+ allocate(ccthet(nsingle,ntheterm2,-nthetyp-1:nthetyp+1,&
+ -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
+ allocate(ddthet(nsingle,ntheterm2,-nthetyp-1:nthetyp+1,&
+ -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
+ allocate(eethet(nsingle,ntheterm2,-nthetyp-1:nthetyp+1,&
+ -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
!(maxsingle,maxtheterm2,-maxthetyp1:maxthetyp1,&
! -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
- allocate(ffthet(ndouble,ndouble,ntheterm3,-maxthetyp1:maxthetyp1,&
- -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
- allocate(ggthet(ndouble,ndouble,ntheterm3,-maxthetyp1:maxthetyp1,&
- -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
+ allocate(ffthet(ndouble,ndouble,ntheterm3,-nthetyp-1:nthetyp+1,&
+ -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
+ allocate(ggthet(ndouble,ndouble,ntheterm3,-nthetyp-1:nthetyp+1,&
+ -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
!(maxdouble,maxdouble,maxtheterm3,-maxthetyp1:maxthetyp1,&
! -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
close (ithep_pdb)
#endif
close(ithep)
+!--------------- Reading theta parameters for nucleic acid-------
+ read (ithep_nucl,*,err=111,end=111) nthetyp_nucl,ntheterm_nucl,&
+ ntheterm2_nucl,ntheterm3_nucl,nsingle_nucl,ndouble_nucl
+ nntheterm_nucl=max0(ntheterm_nucl,ntheterm2_nucl,ntheterm3_nucl)
+ allocate(ithetyp_nucl(ntyp1_molec(2))) !(-ntyp1:ntyp1)
+ allocate(aa0thet_nucl(nthetyp_nucl+1,&
+ nthetyp_nucl+1,nthetyp_nucl+1))
+!(-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
+ allocate(aathet_nucl(ntheterm_nucl+1,nthetyp_nucl+1,&
+ nthetyp_nucl+1,nthetyp_nucl+1))
+!(maxtheterm,-maxthetyp1:maxthetyp1,&
+! -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
+ allocate(bbthet_nucl(nsingle_nucl+1,ntheterm2_nucl+1,nthetyp_nucl+1,&
+ nthetyp_nucl+1,nthetyp_nucl+1))
+ allocate(ccthet_nucl(nsingle_nucl+1,ntheterm2_nucl+1,nthetyp_nucl+1,&
+ nthetyp_nucl+1,nthetyp_nucl+1))
+ allocate(ddthet_nucl(nsingle_nucl+1,ntheterm2_nucl+1,nthetyp_nucl+1,&
+ nthetyp_nucl+1,nthetyp_nucl+1))
+ allocate(eethet_nucl(nsingle_nucl+1,ntheterm2_nucl+1,nthetyp_nucl+1,&
+ nthetyp_nucl+1,nthetyp_nucl+1))
+!(maxsingle,maxtheterm2,-maxthetyp1:maxthetyp1,&
+! -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
+ allocate(ffthet_nucl(ndouble_nucl+1,ndouble_nucl+1,ntheterm3_nucl+1,&
+ nthetyp_nucl+1,nthetyp_nucl+1,nthetyp_nucl+1))
+ allocate(ggthet_nucl(ndouble_nucl+1,ndouble_nucl+1,ntheterm3_nucl+1,&
+ nthetyp_nucl+1,nthetyp_nucl+1,nthetyp_nucl+1))
+
+!(maxdouble,maxdouble,maxtheterm3,-maxthetyp1:maxthetyp1,&
+! -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
+
+ read (ithep_nucl,*,err=111,end=111) (ithetyp_nucl(i),i=1,ntyp1_molec(2))
+
+ aa0thet_nucl(:,:,:)=0.0d0
+ aathet_nucl(:,:,:,:)=0.0d0
+ bbthet_nucl(:,:,:,:,:)=0.0d0
+ ccthet_nucl(:,:,:,:,:)=0.0d0
+ ddthet_nucl(:,:,:,:,:)=0.0d0
+ eethet_nucl(:,:,:,:,:)=0.0d0
+ ffthet_nucl(:,:,:,:,:,:)=0.0d0
+ ggthet_nucl(:,:,:,:,:,:)=0.0d0
+
+ do i=1,nthetyp_nucl
+ do j=1,nthetyp_nucl
+ do k=1,nthetyp_nucl
+ read (ithep_nucl,'(3a)',end=111,err=111) t1,t2,t3
+ read (ithep_nucl,*,end=111,err=111) aa0thet_nucl(i,j,k)
+ read (ithep_nucl,*,end=111,err=111)(aathet_nucl(l,i,j,k),l=1,ntheterm_nucl)
+ read (ithep_nucl,*,end=111,err=111) &
+ (((bbthet_nucl(lll,ll,i,j,k),lll=1,nsingle_nucl), &
+ (ccthet_nucl(lll,ll,i,j,k),lll=1,nsingle_nucl), &
+ (ddthet_nucl(lll,ll,i,j,k),lll=1,nsingle_nucl), &
+ (eethet_nucl(lll,ll,i,j,k),lll=1,nsingle_nucl)),ll=1,ntheterm2_nucl)
+ read (ithep_nucl,*,end=111,err=111) &
+ (((ffthet_nucl(llll,lll,ll,i,j,k),ffthet_nucl(lll,llll,ll,i,j,k), &
+ ggthet_nucl(llll,lll,ll,i,j,k),ggthet_nucl(lll,llll,ll,i,j,k), &
+ llll=1,lll-1),lll=2,ndouble_nucl),ll=1,ntheterm3_nucl)
+ enddo
+ enddo
+ enddo
!-------------------------------------------
allocate(nlob(ntyp1)) !(ntyp1)
nlobi=nlob(i)
if (nlobi.gt.0) then
if (LaTeX) then
- write (iout,'(/3a,i2,a,f8.3)') 'Residue type: ',restyp(i),&
+ write (iout,'(/3a,i2,a,f8.3)') 'Residue type: ',restyp(i,1),&
' # of gaussian lobes:',nlobi,' dsc:',dsc(i)
write (iout,'(1h&,a,3(2h&&,f8.3,2h&&))') &
'log h',(bsc(j,i),j=1,nlobi)
enddo
endif
enddo
+!---------reading nucleic acid parameters for rotamers-------------------
+ allocate(sc_parmin_nucl(9,ntyp_molec(2))) !(maxsccoef,ntyp)
+ do i=1,ntyp_molec(2)
+ read (irotam_nucl,*,end=112,err=112)
+ do j=1,9
+ read(irotam_nucl,*,end=112,err=112) sc_parmin_nucl(j,i)
+ enddo
+ enddo
+ close(irotam_nucl)
+ if (lprint) then
+ write (iout,*)
+ write (iout,*) "Base rotamer parameters"
+ do i=1,ntyp_molec(2)
+ write (iout,'(a)') restyp(i,2)
+ write (iout,'(i5,f10.5)') (i,sc_parmin_nucl(j,i),j=1,9)
+ enddo
+ endif
+
!
! Read the parameters of the probability distribution/energy expression
! of the side chains.
do i=-ntyp,-1
itortyp(i)=-itortyp(-i)
enddo
-! itortyp(ntyp1)=ntortyp
-! itortyp(-ntyp1)=-ntortyp
+ itortyp(ntyp1)=ntortyp
+ itortyp(-ntyp1)=-ntortyp
do iblock=1,2
write (iout,*) 'ntortyp',ntortyp
do i=0,ntortyp-1
enddo
endif
#endif
+ allocate(itortyp_nucl(ntyp1_molec(2))) !(-ntyp1:ntyp1)
+ read (itorp_nucl,*,end=113,err=113) ntortyp_nucl
+! print *,"ntortyp_nucl",ntortyp_nucl,ntyp_molec(2)
+!el from energy module---------
+ allocate(nterm_nucl(ntortyp_nucl,ntortyp_nucl)) !(-maxtor:maxtor,-maxtor:maxtor,2)
+ allocate(nlor_nucl(ntortyp_nucl,ntortyp_nucl)) !(-maxtor:maxtor,-maxtor:maxtor,2)
+
+ allocate(vlor1_nucl(maxlor,ntortyp_nucl,ntortyp_nucl)) !(maxlor,-maxtor:maxtor,-maxtor:maxtor)
+ allocate(vlor2_nucl(maxlor,ntortyp_nucl,ntortyp_nucl))
+ allocate(vlor3_nucl(maxlor,ntortyp_nucl,ntortyp_nucl)) !(maxlor,maxtor,maxtor)
+ allocate(v0_nucl(ntortyp_nucl,ntortyp_nucl)) !(-maxtor:maxtor,-maxtor:maxtor,2)
+
+ allocate(v1_nucl(maxterm,ntortyp_nucl,ntortyp_nucl))
+ allocate(v2_nucl(maxterm,ntortyp_nucl,ntortyp_nucl)) !(maxterm,-maxtor:maxtor,-maxtor:maxtor,2)
+!el---------------------------
+ nterm_nucl(:,:)=0
+ nlor_nucl(:,:)=0
+!el--------------------
+ read (itorp_nucl,*,end=113,err=113) &
+ (itortyp_nucl(i),i=1,ntyp_molec(2))
+! print *,itortyp_nucl(:)
+!c write (iout,*) 'ntortyp',ntortyp
+ do i=1,ntortyp_nucl
+ do j=1,ntortyp_nucl
+ read (itorp_nucl,*,end=113,err=113) nterm_nucl(i,j),nlor_nucl(i,j)
+! print *,nterm_nucl(i,j),nlor_nucl(i,j)
+ v0ij=0.0d0
+ si=-1.0d0
+ do k=1,nterm_nucl(i,j)
+ read (itorp_nucl,*,end=113,err=113) kk,v1_nucl(k,i,j),v2_nucl(k,i,j)
+ v0ij=v0ij+si*v1_nucl(k,i,j)
+ si=-si
+ enddo
+ do k=1,nlor_nucl(i,j)
+ read (itorp,*,end=113,err=113) kk,vlor1_nucl(k,i,j),&
+ vlor2_nucl(k,i,j),vlor3_nucl(k,i,j)
+ v0ij=v0ij+vlor1_nucl(k,i,j)/(1+vlor3_nucl(k,i,j)**2)
+ enddo
+ v0_nucl(i,j)=v0ij
+ enddo
+ enddo
+
! Read of Side-chain backbone correlation parameters
! Modified 11 May 2012 by Adasko
!CC
#endif
if (lprint) then
+ l=3
write (iout,'(/a/)') 'Torsional constants:'
do i=1,nsccortyp
do j=1,nsccortyp
do i=0,nloctyp-1
read (ifourier,*,end=115,err=115)
- read (ifourier,*,end=115,err=115) (b(ii),ii=1,13)
+ read (ifourier,*,end=115,err=115) (buse(ii),ii=1,13)
if (lprint) then
write (iout,*) 'Type',i
- write (iout,'(a,i2,a,f10.5)') ('b(',ii,')=',b(ii),ii=1,13)
+ write (iout,'(a,i2,a,f10.5)') ('buse(',ii,')=',buse(ii),ii=1,13)
endif
- B1(1,i) = b(3)
- B1(2,i) = b(5)
- B1(1,-i) = b(3)
- B1(2,-i) = -b(5)
-! b1(1,i)=0.0d0
-! 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)
-! b1tilde(1,i)=0.0d0
-! 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)
-
-! b2(1,i)=0.0d0
-! 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)
+ B1(1,i) = buse(3)
+ B1(2,i) = buse(5)
+ B1(1,-i) = buse(3)
+ B1(2,-i) = -buse(5)
+! buse1(1,i)=0.0d0
+! buse1(2,i)=0.0d0
+ B1tilde(1,i) = buse(3)
+ B1tilde(2,i) =-buse(5)
+ B1tilde(1,-i) =-buse(3)
+ B1tilde(2,-i) =buse(5)
+! buse1tilde(1,i)=0.0d0
+! buse1tilde(2,i)=0.0d0
+ B2(1,i) = buse(2)
+ B2(2,i) = buse(4)
+ B2(1,-i) =buse(2)
+ B2(2,-i) =-buse(4)
+
+! buse2(1,i)=0.0d0
+! buse2(2,i)=0.0d0
+ CC(1,1,i)= buse(7)
+ CC(2,2,i)=-buse(7)
+ CC(2,1,i)= buse(9)
+ CC(1,2,i)= buse(9)
+ CC(1,1,-i)= buse(7)
+ CC(2,2,-i)=-buse(7)
+ CC(2,1,-i)=-buse(9)
+ CC(1,2,-i)=-buse(9)
! CC(1,1,i)=0.0d0
! CC(2,2,i)=0.0d0
! CC(2,1,i)=0.0d0
! 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)
+ Ctilde(1,1,i)=buse(7)
+ Ctilde(1,2,i)=buse(9)
+ Ctilde(2,1,i)=-buse(9)
+ Ctilde(2,2,i)=buse(7)
+ Ctilde(1,1,-i)=buse(7)
+ Ctilde(1,2,-i)=-buse(9)
+ Ctilde(2,1,-i)=buse(9)
+ Ctilde(2,2,-i)=buse(7)
! Ctilde(1,1,i)=0.0d0
! Ctilde(1,2,i)=0.0d0
! Ctilde(2,1,i)=0.0d0
! 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)
+ DD(1,1,i)= buse(6)
+ DD(2,2,i)=-buse(6)
+ DD(2,1,i)= buse(8)
+ DD(1,2,i)= buse(8)
+ DD(1,1,-i)= buse(6)
+ DD(2,2,-i)=-buse(6)
+ DD(2,1,-i)=-buse(8)
+ DD(1,2,-i)=-buse(8)
! DD(1,1,i)=0.0d0
! DD(2,2,i)=0.0d0
! DD(2,1,i)=0.0d0
! 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)
+ Dtilde(1,1,i)=buse(6)
+ Dtilde(1,2,i)=buse(8)
+ Dtilde(2,1,i)=-buse(8)
+ Dtilde(2,2,i)=buse(6)
+ Dtilde(1,1,-i)=buse(6)
+ Dtilde(1,2,-i)=-buse(8)
+ Dtilde(2,1,-i)=buse(8)
+ Dtilde(2,2,-i)=buse(6)
! Dtilde(1,1,i)=0.0d0
! Dtilde(1,2,i)=0.0d0
! Dtilde(2,1,i)=0.0d0
! 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)
+ EE(1,1,i)= buse(10)+buse(11)
+ EE(2,2,i)=-buse(10)+buse(11)
+ EE(2,1,i)= buse(12)-buse(13)
+ EE(1,2,i)= buse(12)+buse(13)
+ EE(1,1,-i)= buse(10)+buse(11)
+ EE(2,2,-i)=-buse(10)+buse(11)
+ EE(2,1,-i)=-buse(12)+buse(13)
+ EE(1,2,-i)=-buse(12)-buse(13)
! ee(1,1,i)=1.0d0
! ee(2,2,i)=1.0d0
allocate(eps(ntyp,ntyp),sigmaii(ntyp,ntyp),rs0(ntyp,ntyp)) !(ntyp,ntyp)
allocate(augm(ntyp,ntyp)) !(ntyp,ntyp)
allocate(eps_scp(ntyp,2),rscp(ntyp,2)) !(ntyp,2)
+
allocate(sigma0(ntyp),rr0(ntyp),sigii(ntyp)) !(ntyp)
allocate(chip(ntyp1),alp(ntyp1)) !(ntyp)
-
+ allocate(epslip(ntyp,ntyp))
augm(:,:)=0.0D0
chip(:)=0.0D0
alp(:)=0.0D0
call printmat(ntyp,ntyp,ntyp,iout,restyp,eps)
write (iout,'(/a)') 'One-body parameters:'
write (iout,'(a,4x,a)') 'residue','sigma'
- write (iout,'(a3,6x,f10.5)') (restyp(i),sigma0(i),i=1,ntyp)
+ write (iout,'(a3,6x,f10.5)') (restyp(i,1),sigma0(i),i=1,ntyp)
endif
! goto 50
!----------------------- LJK potential --------------------------------
call printmat(ntyp,ntyp,ntyp,iout,restyp,eps)
write (iout,'(/a)') 'One-body parameters:'
write (iout,'(a,4x,2a)') 'residue',' sigma ',' r0 '
- write (iout,'(a3,6x,2f10.5)') (restyp(i),sigma0(i),rr0(i),&
+ write (iout,'(a3,6x,2f10.5)') (restyp(i,1),sigma0(i),rr0(i),&
i=1,ntyp)
endif
! goto 50
!---------------------- GB or BP potential -----------------------------
case(3:4)
! 30 do i=1,ntyp
+! print *,"I AM in SCELE",scelemode
+ if (scelemode.eq.0) then
do i=1,ntyp
read (isidep,*,end=117,err=117)(eps(i,j),j=i,ntyp)
enddo
read (isidep,*,end=117,err=117)(sigii(i),i=1,ntyp)
read (isidep,*,end=117,err=117)(chip(i),i=1,ntyp)
read (isidep,*,end=117,err=117)(alp(i),i=1,ntyp)
+ do i=1,ntyp
+ read (isidep,*,end=117,err=117)(epslip(i,j),j=i,ntyp)
+ enddo
+
! For the GB potential convert sigma'**2 into chi'
if (ipot.eq.4) then
do i=1,ntyp
write (iout,'(/a)') 'One-body parameters:'
write (iout,'(a,4x,4a)') 'residue',' sigma ','s||/s_|_^2',&
' chip ',' alph '
- write (iout,'(a3,6x,4f10.5)') (restyp(i),sigma0(i),sigii(i),&
+ write (iout,'(a3,6x,4f10.5)') (restyp(i,1),sigma0(i),sigii(i),&
chip(i),alp(i),i=1,ntyp)
endif
+ else
+! print *,ntyp,"NTYP"
+ allocate(icharge(ntyp1))
+! print *,ntyp,icharge(i)
+ icharge(:)=0
+ read (isidep,*) (icharge(i),i=1,ntyp)
+ print *,ntyp,icharge(i)
+! if(.not.allocated(eps)) allocate(eps(-ntyp
+!c write (2,*) "icharge",(icharge(i),i=1,ntyp)
+ allocate(alphapol(ntyp,ntyp),epshead(ntyp,ntyp),sig0head(ntyp,ntyp))
+ allocate(sigiso1(ntyp,ntyp),rborn(ntyp,ntyp),sigmap1(ntyp,ntyp))
+ allocate(sigmap2(ntyp,ntyp),sigiso2(ntyp,ntyp))
+ allocate(chis(ntyp,ntyp),wquad(ntyp,ntyp),chipp(ntyp,ntyp))
+ allocate(epsintab(ntyp,ntyp))
+ allocate(dtail(2,ntyp,ntyp))
+ allocate(alphasur(4,ntyp,ntyp),alphiso(4,ntyp,ntyp))
+ allocate(wqdip(2,ntyp,ntyp))
+ allocate(wstate(4,ntyp,ntyp))
+ allocate(dhead(2,2,ntyp,ntyp))
+ allocate(nstate(ntyp,ntyp))
+ if (.not.allocated(sigma)) allocate(sigma(0:ntyp1,0:ntyp1))
+ if (.not.allocated(chi)) allocate(chi(ntyp1,ntyp1)) !(ntyp,ntyp)
+ do i=1,ntyp
+ do j=1,i
+! write (*,*) "Im in ALAB", i, " ", j
+ read(isidep,*) &
+ eps(i,j),sigma(i,j),chi(i,j),chi(j,i),chipp(i,j),chipp(j,i), &
+ (alphasur(k,i,j),k=1,4),sigmap1(i,j),sigmap2(i,j), &
+ chis(i,j),chis(j,i), &
+ nstate(i,j),(wstate(k,i,j),k=1,4), &
+ dhead(1,1,i,j),dhead(1,2,i,j),dhead(2,1,i,j),dhead(2,2,i,j),&
+ dtail(1,i,j),dtail(2,i,j), &
+ epshead(i,j),sig0head(i,j), &
+ rborn(i,j),rborn(j,i),(wqdip(k,i,j),k=1,2),wquad(i,j), &
+ alphapol(i,j),alphapol(j,i), &
+ (alphiso(k,i,j),k=1,4),sigiso1(i,j),sigiso2(i,j),epsintab(i,j)
+! print *,eps(i,j),sigma(i,j),"SIGMAP",i,j,sigmap1(i,j),sigmap2(j,i)
+ END DO
+ END DO
+ DO i = 1, ntyp
+ DO j = i+1, ntyp
+ eps(i,j) = eps(j,i)
+ sigma(i,j) = sigma(j,i)
+ sigmap1(i,j)=sigmap1(j,i)
+ sigmap2(i,j)=sigmap2(j,i)
+ sigiso1(i,j)=sigiso1(j,i)
+ sigiso2(i,j)=sigiso2(j,i)
+! print *,"ATU",sigma(j,i),sigma(i,j),i,j
+ nstate(i,j) = nstate(j,i)
+ dtail(1,i,j) = dtail(1,j,i)
+ dtail(2,i,j) = dtail(2,j,i)
+ DO k = 1, 4
+ alphasur(k,i,j) = alphasur(k,j,i)
+ wstate(k,i,j) = wstate(k,j,i)
+ alphiso(k,i,j) = alphiso(k,j,i)
+ END DO
+
+ dhead(2,1,i,j) = dhead(1,1,j,i)
+ dhead(2,2,i,j) = dhead(1,2,j,i)
+ dhead(1,1,i,j) = dhead(2,1,j,i)
+ dhead(1,2,i,j) = dhead(2,2,j,i)
+
+ epshead(i,j) = epshead(j,i)
+ sig0head(i,j) = sig0head(j,i)
+
+ DO k = 1, 2
+ wqdip(k,i,j) = wqdip(k,j,i)
+ END DO
+
+ wquad(i,j) = wquad(j,i)
+ epsintab(i,j) = epsintab(j,i)
+! if (epsintab(i,j).ne.1.0) print *,"WHAT?",i,j,epsintab(i,j)
+ END DO
+ END DO
+ endif
! goto 50
!--------------------- GBV potential -----------------------------------
case(5)
write (iout,'(/a)') 'One-body parameters:'
write (iout,'(a,4x,5a)') 'residue',' sigma ',' r0 ',&
's||/s_|_^2',' chip ',' alph '
- write (iout,'(a3,6x,5f10.5)') (restyp(i),sigma0(i),rr0(i),&
+ write (iout,'(a3,6x,5f10.5)') (restyp(i,1),sigma0(i),rr0(i),&
sigii(i),chip(i),alp(i),i=1,ntyp)
endif
case default
end select
continue
close (isidep)
+
!-----------------------------------------------------------------------
! Calculate the "working" parameters of SC interactions.
!el from module energy - COMMON.INTERACT-------
- allocate(aa(ntyp1,ntyp1),bb(ntyp1,ntyp1),chi(ntyp1,ntyp1)) !(ntyp,ntyp)
- allocate(sigma(0:ntyp1,0:ntyp1),r0(ntyp1,ntyp1)) !(0:ntyp1,0:ntyp1)
- aa(:,:)=0.0D0
- bb(:,:)=0.0D0
+ allocate(aa_aq(ntyp1,ntyp1),bb_aq(ntyp1,ntyp1))
+ if (.not.allocated(chi)) allocate(chi(ntyp1,ntyp1)) !(ntyp,ntyp)
+ allocate(aa_lip(ntyp1,ntyp1),bb_lip(ntyp1,ntyp1)) !(ntyp,ntyp)
+ if (.not.allocated(sigma)) allocate(sigma(0:ntyp1,0:ntyp1))
+ allocate(r0(ntyp1,ntyp1)) !(0:ntyp1,0:ntyp1)
+ allocate(acavtub(ntyp1),bcavtub(ntyp1),ccavtub(ntyp1),&
+ dcavtub(ntyp1))
+ allocate(sc_aa_tube_par(ntyp1),sc_bb_tube_par(ntyp1),&
+ tubetranene(ntyp1))
+ aa_aq(:,:)=0.0D0
+ bb_aq(:,:)=0.0D0
+ aa_lip(:,:)=0.0D0
+ bb_lip(:,:)=0.0D0
+ if (scelemode.eq.0) then
chi(:,:)=0.0D0
sigma(:,:)=0.0D0
r0(:,:)=0.0D0
-
+ endif
+ acavtub(:)=0.0d0
+ bcavtub(:)=0.0d0
+ ccavtub(:)=0.0d0
+ dcavtub(:)=0.0d0
+ sc_aa_tube_par(:)=0.0d0
+ sc_bb_tube_par(:)=0.0d0
+
!--------------------------------
do i=2,ntyp
do j=1,i-1
eps(i,j)=eps(j,i)
+ epslip(i,j)=epslip(j,i)
enddo
enddo
+ if (scelemode.eq.0) then
do i=1,ntyp
do j=i,ntyp
sigma(i,j)=dsqrt(sigma0(i)**2+sigma0(j)**2)
rs0(j,i)=rs0(i,j)
enddo
enddo
+ endif
if (lprint) write (iout,'(/a/10x,7a/72(1h-))') &
'Working parameters of the SC interactions:',&
' a ',' b ',' augm ',' sigma ',' r0 ',&
epsij=eps(i,j)
if (ipot.eq.1 .or. ipot.eq.3 .or. ipot.eq.4) then
rrij=sigma(i,j)
+! print *,"SIGMA ZLA?",sigma(i,j)
else
rrij=rr0(i)+rr0(j)
endif
epsij=eps(i,j)
sigeps=dsign(1.0D0,epsij)
epsij=dabs(epsij)
- aa(i,j)=epsij*rrij*rrij
- bb(i,j)=-sigeps*epsij*rrij
- aa(j,i)=aa(i,j)
- bb(j,i)=bb(i,j)
- if (ipot.gt.2) then
+ aa_aq(i,j)=epsij*rrij*rrij
+ print *,"ADASKO",epsij,rrij,expon
+ bb_aq(i,j)=-sigeps*epsij*rrij
+ aa_aq(j,i)=aa_aq(i,j)
+ bb_aq(j,i)=bb_aq(i,j)
+ epsijlip=epslip(i,j)
+ sigeps=dsign(1.0D0,epsijlip)
+ epsijlip=dabs(epsijlip)
+ aa_lip(i,j)=epsijlip*rrij*rrij
+ bb_lip(i,j)=-sigeps*epsijlip*rrij
+ aa_lip(j,i)=aa_lip(i,j)
+ bb_lip(j,i)=bb_lip(i,j)
+!C write(iout,*) aa_lip
+ if ((ipot.gt.2).and. (scelemode.eq.0)) then
sigt1sq=sigma0(i)**2
sigt2sq=sigma0(j)**2
sigii1=sigii(i)
endif
if (lprint) then
write (iout,'(2(a3,2x),3(1pe10.3),5(0pf8.3))') &
- restyp(i),restyp(j),aa(i,j),bb(i,j),augm(i,j),&
+ restyp(i,1),restyp(j,1),aa_aq(i,j),bb_aq(i,j),augm(i,j),&
sigma(i,j),r0(i,j),chi(i,j),chi(j,i)
endif
enddo
enddo
+ allocate(eps_nucl(ntyp_molec(2),ntyp_molec(2)))
+ allocate(sigma_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp_molec(2),ntyp_molec(2))
+ allocate(elpp6_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp_molec(2),ntyp_molec(2))
+ allocate(elpp3_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp,2)
+ allocate(elpp63_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp_molec(2),ntyp_molec(2))
+ allocate(elpp32_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp,2)
+ allocate(chi_nucl(ntyp_molec(2),ntyp_molec(2)),chip_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp_molec(2),ntyp_molec(2))
+ allocate(ael3_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp,2)
+ allocate(ael6_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp,2)
+ allocate(ael32_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp,2)
+ allocate(ael63_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp,2)
+ allocate(aa_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp,2)
+ allocate(bb_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp,2)
+ allocate(r0_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp,2)
+ allocate(sigmaii_nucl(ntyp_molec(2),ntyp_molec(2))) !(ntyp_molec(2),ntyp_molec(2))
+ allocate(eps_scp_nucl(ntyp_molec(2)),rscp_nucl(ntyp_molec(2))) !(ntyp,2)
+
+! augm(:,:)=0.0D0
+! chip(:)=0.0D0
+! alp(:)=0.0D0
+! sigma0(:)=0.0D0
+! sigii(:)=0.0D0
+! rr0(:)=0.0D0
+
+ read (isidep_nucl,*) ipot_nucl
+! print *,"TU?!",ipot_nucl
+ if (ipot_nucl.eq.1) then
+ do i=1,ntyp_molec(2)
+ do j=i,ntyp_molec(2)
+ read (isidep_nucl,*) eps_nucl(i,j),sigma_nucl(i,j),elpp6_nucl(i,j),&
+ elpp3_nucl(i,j), elpp63_nucl(i,j),elpp32_nucl(i,j)
+ enddo
+ enddo
+ else
+ do i=1,ntyp_molec(2)
+ do j=i,ntyp_molec(2)
+ read (isidep_nucl,*) eps_nucl(i,j),sigma_nucl(i,j),chi_nucl(i,j),&
+ chi_nucl(j,i),chip_nucl(i,j),chip_nucl(j,i),&
+ elpp6_nucl(i,j),elpp3_nucl(i,j),elpp63_nucl(i,j),elpp32_nucl(i,j)
+ enddo
+ enddo
+ endif
+! rpp(1,1)=2**(1.0/6.0)*5.16158
+ do i=1,ntyp_molec(2)
+ do j=i,ntyp_molec(2)
+ rrij=sigma_nucl(i,j)
+ r0_nucl(i,j)=rrij
+ r0_nucl(j,i)=rrij
+ rrij=rrij**expon
+ epsij=4*eps_nucl(i,j)
+ sigeps=dsign(1.0D0,epsij)
+ epsij=dabs(epsij)
+ aa_nucl(i,j)=epsij*rrij*rrij
+ bb_nucl(i,j)=-sigeps*epsij*rrij
+ ael3_nucl(i,j)=elpp3_nucl(i,j)*dsqrt(rrij)
+ ael6_nucl(i,j)=elpp6_nucl(i,j)*rrij
+ ael63_nucl(i,j)=elpp63_nucl(i,j)*rrij
+ ael32_nucl(i,j)=elpp32_nucl(i,j)*rrij
+ sigmaii_nucl(i,j)=sigma_nucl(i,j)/sqrt(1-(chi_nucl(i,j)+chi_nucl(j,i)- &
+ 2*chi_nucl(i,j)*chi_nucl(j,i))/(1-chi_nucl(i,j)*chi_nucl(j,i)))
+ enddo
+ do j=1,i-1
+ aa_nucl(i,j)=aa_nucl(j,i)
+ bb_nucl(i,j)=bb_nucl(j,i)
+ ael3_nucl(i,j)=ael3_nucl(j,i)
+ ael6_nucl(i,j)=ael6_nucl(j,i)
+ ael63_nucl(i,j)=ael63_nucl(j,i)
+ ael32_nucl(i,j)=ael32_nucl(j,i)
+ elpp3_nucl(i,j)=elpp3_nucl(j,i)
+ elpp6_nucl(i,j)=elpp6_nucl(j,i)
+ elpp63_nucl(i,j)=elpp63_nucl(j,i)
+ elpp32_nucl(i,j)=elpp32_nucl(j,i)
+ eps_nucl(i,j)=eps_nucl(j,i)
+ sigma_nucl(i,j)=sigma_nucl(j,i)
+ sigmaii_nucl(i,j)=sigmaii_nucl(j,i)
+ enddo
+ enddo
+
+ write(iout,*) "tube param"
+ read(itube,*) epspeptube,sigmapeptube,acavtubpep,bcavtubpep, &
+ ccavtubpep,dcavtubpep,tubetranenepep
+ sigmapeptube=sigmapeptube**6
+ sigeps=dsign(1.0D0,epspeptube)
+ epspeptube=dabs(epspeptube)
+ pep_aa_tube=4.0d0*epspeptube*sigmapeptube**2
+ pep_bb_tube=-sigeps*4.0d0*epspeptube*sigmapeptube
+ write(iout,*) pep_aa_tube,pep_bb_tube,tubetranenepep
+ do i=1,ntyp
+ read(itube,*) epssctube,sigmasctube,acavtub(i),bcavtub(i), &
+ ccavtub(i),dcavtub(i),tubetranene(i)
+ sigmasctube=sigmasctube**6
+ sigeps=dsign(1.0D0,epssctube)
+ epssctube=dabs(epssctube)
+ sc_aa_tube_par(i)=4.0d0*epssctube*sigmasctube**2
+ sc_bb_tube_par(i)=-sigeps*4.0d0*epssctube*sigmasctube
+ write(iout,*) sc_aa_tube_par(i), sc_bb_tube_par(i),tubetranene(i)
+ enddo
+!-----------------READING SC BASE POTENTIALS-----------------------------
+ allocate(eps_scbase(ntyp_molec(1),ntyp_molec(2)))
+ allocate(sigma_scbase(ntyp_molec(1),ntyp_molec(2)))
+ allocate(chi_scbase(ntyp_molec(1),ntyp_molec(2),2))
+ allocate(chipp_scbase(ntyp_molec(1),ntyp_molec(2),2))
+ allocate(alphasur_scbase(4,ntyp_molec(1),ntyp_molec(2)))
+ allocate(sigmap1_scbase(ntyp_molec(1),ntyp_molec(2)))
+ allocate(sigmap2_scbase(ntyp_molec(1),ntyp_molec(2)))
+ allocate(chis_scbase(ntyp_molec(1),ntyp_molec(2),2))
+ allocate(dhead_scbasei(ntyp_molec(1),ntyp_molec(2)))
+ allocate(dhead_scbasej(ntyp_molec(1),ntyp_molec(2)))
+ allocate(rborn_scbasei(ntyp_molec(1),ntyp_molec(2)))
+ allocate(rborn_scbasej(ntyp_molec(1),ntyp_molec(2)))
+ allocate(wdipdip_scbase(3,ntyp_molec(1),ntyp_molec(2)))
+ allocate(wqdip_scbase(2,ntyp_molec(1),ntyp_molec(2)))
+ allocate(alphapol_scbase(ntyp_molec(1),ntyp_molec(2)))
+ allocate(epsintab_scbase(ntyp_molec(1),ntyp_molec(2)))
+
+
+ do i=1,ntyp_molec(1)
+ do j=1,ntyp_molec(2)-1 ! without U then we will take T for U
+ write (*,*) "Im in ", i, " ", j
+ read(isidep_scbase,*) &
+ eps_scbase(i,j),sigma_scbase(i,j),chi_scbase(i,j,1),&
+ chi_scbase(i,j,2),chipp_scbase(i,j,1),chipp_scbase(i,j,2)
+ write(*,*) "eps",eps_scbase(i,j)
+ read(isidep_scbase,*) &
+ (alphasur_scbase(k,i,j),k=1,4),sigmap1_scbase(i,j),sigmap2_scbase(i,j), &
+ chis_scbase(i,j,1),chis_scbase(i,j,2)
+ read(isidep_scbase,*) &
+ dhead_scbasei(i,j), &
+ dhead_scbasej(i,j), &
+ rborn_scbasei(i,j),rborn_scbasej(i,j)
+ read(isidep_scbase,*) &
+ (wdipdip_scbase(k,i,j),k=1,3), &
+ (wqdip_scbase(k,i,j),k=1,2)
+ read(isidep_scbase,*) &
+ alphapol_scbase(i,j), &
+ epsintab_scbase(i,j)
+ END DO
+ END DO
+ allocate(aa_scbase(ntyp_molec(1),ntyp_molec(2)))
+ allocate(bb_scbase(ntyp_molec(1),ntyp_molec(2)))
+
+ do i=1,ntyp_molec(1)
+ do j=1,ntyp_molec(2)-1
+ epsij=eps_scbase(i,j)
+ rrij=sigma_scbase(i,j)
+! r0(i,j)=rrij
+! r0(j,i)=rrij
+ rrij=rrij**expon
+! epsij=eps(i,j)
+ sigeps=dsign(1.0D0,epsij)
+ epsij=dabs(epsij)
+ aa_scbase(i,j)=epsij*rrij*rrij
+ bb_scbase(i,j)=-sigeps*epsij*rrij
+ enddo
+ enddo
+!-----------------READING PEP BASE POTENTIALS-------------------
+ allocate(eps_pepbase(ntyp_molec(2)))
+ allocate(sigma_pepbase(ntyp_molec(2)))
+ allocate(chi_pepbase(ntyp_molec(2),2))
+ allocate(chipp_pepbase(ntyp_molec(2),2))
+ allocate(alphasur_pepbase(4,ntyp_molec(2)))
+ allocate(sigmap1_pepbase(ntyp_molec(2)))
+ allocate(sigmap2_pepbase(ntyp_molec(2)))
+ allocate(chis_pepbase(ntyp_molec(2),2))
+ allocate(wdipdip_pepbase(3,ntyp_molec(2)))
+
+
+ do j=1,ntyp_molec(2)-1 ! without U then we will take T for U
+ write (*,*) "Im in ", i, " ", j
+ read(isidep_pepbase,*) &
+ eps_pepbase(j),sigma_pepbase(j),chi_pepbase(j,1),&
+ chi_pepbase(j,2),chipp_pepbase(j,1),chipp_pepbase(j,2)
+ write(*,*) "eps",eps_pepbase(j)
+ read(isidep_pepbase,*) &
+ (alphasur_pepbase(k,j),k=1,4),sigmap1_pepbase(j),sigmap2_pepbase(j), &
+ chis_pepbase(j,1),chis_pepbase(j,2)
+ read(isidep_pepbase,*) &
+ (wdipdip_pepbase(k,j),k=1,3)
+ END DO
+ allocate(aa_pepbase(ntyp_molec(2)))
+ allocate(bb_pepbase(ntyp_molec(2)))
+
+ do j=1,ntyp_molec(2)-1
+ epsij=eps_pepbase(j)
+ rrij=sigma_pepbase(j)
+! r0(i,j)=rrij
+! r0(j,i)=rrij
+ rrij=rrij**expon
+! epsij=eps(i,j)
+ sigeps=dsign(1.0D0,epsij)
+ epsij=dabs(epsij)
+ aa_pepbase(j)=epsij*rrij*rrij
+ bb_pepbase(j)=-sigeps*epsij*rrij
+ enddo
+!--------------READING SC PHOSPHATE-------------------------------------
+ allocate(eps_scpho(ntyp_molec(1)))
+ allocate(sigma_scpho(ntyp_molec(1)))
+ allocate(chi_scpho(ntyp_molec(1),2))
+ allocate(chipp_scpho(ntyp_molec(1),2))
+ allocate(alphasur_scpho(4,ntyp_molec(1)))
+ allocate(sigmap1_scpho(ntyp_molec(1)))
+ allocate(sigmap2_scpho(ntyp_molec(1)))
+ allocate(chis_scpho(ntyp_molec(1),2))
+ allocate(wqq_scpho(ntyp_molec(1)))
+ allocate(wqdip_scpho(2,ntyp_molec(1)))
+ allocate(alphapol_scpho(ntyp_molec(1)))
+ allocate(epsintab_scpho(ntyp_molec(1)))
+ allocate(dhead_scphoi(ntyp_molec(1)))
+ allocate(rborn_scphoi(ntyp_molec(1)))
+ allocate(rborn_scphoj(ntyp_molec(1)))
+ allocate(alphi_scpho(ntyp_molec(1)))
+
+
+! j=1
+ do j=1,ntyp_molec(1) ! without U then we will take T for U
+ write (*,*) "Im in scpho ", i, " ", j
+ read(isidep_scpho,*) &
+ eps_scpho(j),sigma_scpho(j),chi_scpho(j,1),&
+ chi_scpho(j,2),chipp_scpho(j,1),chipp_scpho(j,2)
+ write(*,*) "eps",eps_scpho(j)
+ read(isidep_scpho,*) &
+ (alphasur_scpho(k,j),k=1,4),sigmap1_scpho(j),sigmap2_scpho(j), &
+ chis_scpho(j,1),chis_scpho(j,2)
+ read(isidep_scpho,*) &
+ (wqdip_scpho(k,j),k=1,2),wqq_scpho(j),dhead_scphoi(j)
+ read(isidep_scpho,*) &
+ epsintab_scpho(j),alphapol_scpho(j),rborn_scphoi(j),rborn_scphoj(j), &
+ alphi_scpho(j)
+
+ END DO
+ allocate(aa_scpho(ntyp_molec(1)))
+ allocate(bb_scpho(ntyp_molec(1)))
+
+ do j=1,ntyp_molec(1)
+ epsij=eps_scpho(j)
+ rrij=sigma_scpho(j)
+! r0(i,j)=rrij
+! r0(j,i)=rrij
+ rrij=rrij**expon
+! epsij=eps(i,j)
+ sigeps=dsign(1.0D0,epsij)
+ epsij=dabs(epsij)
+ aa_scpho(j)=epsij*rrij*rrij
+ bb_scpho(j)=-sigeps*epsij*rrij
+ enddo
+
+
+ read(isidep_peppho,*) &
+ eps_peppho,sigma_peppho
+ read(isidep_peppho,*) &
+ (alphasur_peppho(k),k=1,4),sigmap1_peppho,sigmap2_peppho
+ read(isidep_peppho,*) &
+ (wqdip_peppho(k),k=1,2)
+
+ epsij=eps_peppho
+ rrij=sigma_peppho
+! r0(i,j)=rrij
+! r0(j,i)=rrij
+ rrij=rrij**expon
+! epsij=eps(i,j)
+ sigeps=dsign(1.0D0,epsij)
+ epsij=dabs(epsij)
+ aa_peppho=epsij*rrij*rrij
+ bb_peppho=-sigeps*epsij*rrij
+
+
allocate(aad(ntyp,2),bad(ntyp,2)) !(ntyp,2)
bad(:,:)=0.0D0
endif
! lprint=.false.
#endif
+ allocate(aad_nucl(ntyp_molec(2)),bad_nucl(ntyp_molec(2))) !(ntyp,2)
+
+ do i=1,ntyp_molec(2)
+ read (iscpp_nucl,*,end=118,err=118) eps_scp_nucl(i),rscp_nucl(i)
+ enddo
+ do i=1,ntyp_molec(2)
+ aad_nucl(i)=dabs(eps_scp_nucl(i))*rscp_nucl(i)**12
+ bad_nucl(i)=-2*eps_scp_nucl(i)*rscp_nucl(i)**6
+ enddo
+ r0pp=1.12246204830937298142*5.16158
+ epspp=4.95713/4
+ AEES=108.661
+ BEES=0.433246
+
!
! Define the constants of the disulfide bridge
!
write (iout,'(3(a,f10.2))') 'v1ss:',v1ss,' v2ss:',v2ss,&
' v3ss:',v3ss
endif
+ if (shield_mode.gt.0) then
+ pi=4.0D0*datan(1.0D0)
+!C VSolvSphere the volume of solving sphere
+ print *,pi,"pi"
+!C rpp(1,1) is the energy r0 for peptide group contact and will be used for it
+!C there will be no distinction between proline peptide group and normal peptide
+!C group in case of shielding parameters
+ VSolvSphere=4.0/3.0*pi*(4.50d0)**3
+ VSolvSphere_div=VSolvSphere-4.0/3.0*pi*(4.50/2.0)**3
+ write (iout,*) VSolvSphere,VSolvSphere_div
+!C long axis of side chain
+ do i=1,ntyp
+ long_r_sidechain(i)=vbldsc0(1,i)
+! if (scelemode.eq.0) then
+ short_r_sidechain(i)=sigma(i,i)/sqrt(2.0)
+ if (short_r_sidechain(i).eq.0.0) short_r_sidechain(i)=0.2
+! else
+! short_r_sidechain(i)=sigma(i,i)
+! endif
+ write(iout,*) "parame for long and short axis",i,vbldsc0(1,i),&
+ sigma0(i)
+ enddo
+ buff_shield=1.0d0
+ endif
+
return
111 write (iout,*) "Error reading bending energy parameters."
goto 999
! Read the PDB file and convert the peptide geometry into virtual-chain
! geometry.
use geometry_data
- use energy_data, only: itype
+ use energy_data, only: itype,istype
use control_data
use compare_data
use MPI_data
- use control, only: rescode
+! use control, only: rescode,sugarcode
! implicit real*8 (a-h,o-z)
! include 'DIMENSIONS'
! include 'COMMON.LOCAL'
! include 'COMMON.CONTROL'
! include 'COMMON.DISTFIT'
! include 'COMMON.SETUP'
- integer :: i,j,ibeg,ishift1,ires,iii,ires_old,ishift!,ity!,&
+ integer :: i,j,ibeg,ishift1,ires,iii,ires_old,ishift,k!,ity!,&
! ishift_pdb
logical :: lprn=.true.,fail
real(kind=8),dimension(3) :: e1,e2,e3
character(len=5) :: atom
character(len=80) :: card
real(kind=8),dimension(3,20) :: sccor
- integer :: kkk,lll,icha,kupa !rescode,
+ integer :: kkk,lll,icha,kupa,molecule,counter,seqalingbegin !rescode,
+ integer :: isugar,molecprev,firstion
+ character*1 :: sugar
real(kind=8) :: cou
+ real(kind=8),dimension(3) :: ccc
!el local varables
integer,dimension(2,maxres/3) :: hfrag_alloc
integer,dimension(4,maxres/3) :: bfrag_alloc
real(kind=8),dimension(3,maxres2+2,maxperm) :: cref_alloc !(3,maxres2+2,maxperm)
-
+ real(kind=8),dimension(:,:), allocatable :: c_temporary
+ integer,dimension(:,:) , allocatable :: itype_temporary
+ integer,dimension(:),allocatable :: istype_temp
efree_temp=0.0d0
ibeg=1
ishift1=0
ishift=0
+ molecule=1
+ counter=0
! write (2,*) "UNRES_PDB",unres_pdb
ires=0
ires_old=0
+#ifdef WHAM_RUN
+ do i=1,nres
+ do j=1,5
+ itype(i,j)=0
+ enddo
+ enddo
+#endif
nres=0
iii=0
lsecondary=.false.
nhfrag=0
nbfrag=0
+ do j=1,5
+ nres_molec(j)=0
+ enddo
+
+
!-----------------------------
allocate(hfrag(2,maxres/3)) !(2,maxres/3)
allocate(bfrag(4,maxres/3)) !(4,maxres/3)
-
+ if(.not. allocated(istype)) allocate(istype(maxres))
do i=1,100000
read (ipdbin,'(a80)',end=10) card
-! write (iout,'(a)') card
+ write (iout,'(a)') card
if (card(:5).eq.'HELIX') then
nhfrag=nhfrag+1
lsecondary=.true.
goto 10
else if (card(:3).eq.'TER') then
! End current chain
- ires_old=ires+1
+ ires_old=ires+2
+ ishift=ishift+1
ishift1=ishift1+1
- itype(ires_old)=ntyp1
+ itype(ires_old,molecule)=ntyp1_molec(molecule)
+ itype(ires_old-1,molecule)=ntyp1_molec(molecule)
+ nres_molec(molecule)=nres_molec(molecule)+2
ibeg=2
! write (iout,*) "Chain ended",ires,ishift,ires_old
if (unres_pdb) then
enddo
else
call sccenter(ires,iii,sccor)
+! iii=0
endif
iii=0
endif
! Read free energy
if (index(card,"FREE ENERGY").gt.0) read(card(35:),*) efree_temp
! Fish out the ATOM cards.
+! write(iout,*) 'card',card(1:20)
if (index(card(1:4),'ATOM').gt.0) then
read (card(12:16),*) atom
! write (iout,*) "! ",atom," !",ires
! write (iout,*) "Calculating sidechain center iii",iii
if (unres_pdb) then
do j=1,3
- dc(j,ires+nres)=sccor(j,iii)
+ dc(j,ires+ishift1-ishift-1)=sccor(j,iii)
enddo
else
call sccenter(ires_old,iii,sccor)
ishift=ires-1
if (res.ne.'GLY' .and. res.ne. 'ACE') then
ishift=ishift-1
- itype(1)=ntyp1
+ itype(1,1)=ntyp1
+ nres_molec(molecule)=nres_molec(molecule)+1
endif
ires=ires-ishift+ishift1
ires_old=ires
ishift1=ishift1-1 !!!!!
! write (iout,*) "New chain started",ires,ishift,ishift1,"!"
ires=ires-ishift+ishift1
+! print *,ires,ishift,ishift1
ires_old=ires
ibeg=0
else
ishift=ishift-(ires-ishift+ishift1-ires_old-1)
ires=ires-ishift+ishift1
ires_old=ires
- endif
+ endif
+! print *,'atom',ires,atom
if (res.eq.'ACE' .or. res.eq.'NHE') then
- itype(ires)=10
+ itype(ires,1)=10
+ else
+ if (atom.eq.'CA '.or.atom.eq.'N ') then
+ molecule=1
+ itype(ires,molecule)=rescode(ires,res,0,molecule)
+ firstion=0
+! nres_molec(molecule)=nres_molec(molecule)+1
else
- itype(ires)=rescode(ires,res,0)
+ molecule=2
+ itype(ires,molecule)=rescode(ires,res(2:3),0,molecule)
+! nres_molec(molecule)=nres_molec(molecule)+1
+ read (card(19:19),'(a1)') sugar
+ isugar=sugarcode(sugar,ires)
+! if (ibeg.eq.1) then
+! istype(1)=isugar
+! else
+ istype(ires)=isugar
+! print *,"ires=",ires,istype(ires)
+! endif
+
+ endif
endif
else
ires=ires-ishift+ishift1
if (atom.eq.'CA' .or. atom.eq.'CH3' .or. &
res.eq.'NHE'.and.atom(:2).eq.'HN') then
read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
+! print *,ires,ishift,ishift1
! write (iout,*) "backbone ",atom
#ifdef DEBUG
write (iout,'(2i3,2x,a,3f8.3)') &
- ires,itype(ires),res,(c(j,ires),j=1,3)
+ ires,itype(ires,1),res,(c(j,ires),j=1,3)
#endif
iii=iii+1
+ nres_molec(molecule)=nres_molec(molecule)+1
do j=1,3
sccor(j,iii)=c(j,ires)
enddo
-! write (*,*) card(23:27),ires,itype(ires)
+ else if (.not.unres_pdb .and. (atom.eq."C1'" .or. &
+ atom.eq."C2'" .or. atom.eq."C3'" &
+ .or. atom.eq."C4'" .or. atom.eq."O4'")) then
+ read(card(31:54),'(3f8.3)') (ccc(j),j=1,3)
+!c write (2,'(i5,3f10.5)') ires,(ccc(j),j=1,3)
+! print *,ires,ishift,ishift1
+ counter=counter+1
+! iii=iii+1
+! do j=1,3
+! sccor(j,iii)=c(j,ires)
+! enddo
+ do j=1,3
+ c(j,ires)=c(j,ires)+ccc(j)/5.0
+ enddo
+ print *,counter,molecule
+ if (counter.eq.5) then
+! iii=iii+1
+ nres_molec(molecule)=nres_molec(molecule)+1
+ firstion=0
+! do j=1,3
+! sccor(j,iii)=c(j,ires)
+! enddo
+ counter=0
+ endif
+! print *, "ATOM",atom(1:3)
+ else if (atom.eq."C5'") then
+ read (card(19:19),'(a1)') sugar
+ isugar=sugarcode(sugar,ires)
+ if (ibeg.eq.1) then
+ istype(1)=isugar
+ else
+ istype(ires)=isugar
+! print *,ires,istype(ires)
+ endif
+ if (unres_pdb) then
+ molecule=2
+! print *,"nres_molec(molecule)",nres_molec(molecule),ires
+ read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
+ nres_molec(molecule)=nres_molec(molecule)+1
+ print *,"nres_molec(molecule)",nres_molec(molecule),ires
+
+ else
+ iii=iii+1
+ read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
+ endif
+ else if ((atom.eq."C1'").and.unres_pdb) then
+ iii=iii+1
+ read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
+! write (*,*) card(23:27),ires,itype(ires,1)
else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and. &
atom.ne.'N' .and. atom.ne.'C' .and. &
atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and. &
- atom.ne.'OXT' .and. atom(:2).ne.'3H') then
+ atom.ne.'OXT' .and. atom(:2).ne.'3H' &
+ .and. atom.ne.'P '.and. &
+ atom(1:1).ne.'H' .and. &
+ atom.ne.'OP1' .and. atom.ne.'OP2 '.and. atom.ne.'OP3'&
+ ) then
! write (iout,*) "sidechain ",atom
+! write (iout,*) "sidechain ",atom,molecule,ires,atom(3:3)
+ if ((molecule.ne.2).or.(atom(3:3).ne."'")) then
+! write (iout,*) "sidechain ",atom,molecule,ires,atom(3:3)
iii=iii+1
read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
+ endif
endif
- endif
+ else if ((ions).and.(card(1:6).eq.'HETATM')) then
+ if (firstion.eq.0) then
+ firstion=1
+ if (unres_pdb) then
+ do j=1,3
+ dc(j,ires)=sccor(j,iii)
+ enddo
+ else
+ call sccenter(ires,iii,sccor)
+ endif
+ endif
+ read (card(12:16),*) atom
+ print *,"HETATOM", atom
+ read (card(18:20),'(a3)') res
+ if ((atom(1:2).eq.'NA').or.(atom(1:2).eq.'CL').or.&
+ (atom(1:2).eq.'CA').or.(atom(1:2).eq.'MG') &
+ .or.(atom(1:2).eq.'K ')) &
+ then
+ ires=ires+1
+ if (molecule.ne.5) molecprev=molecule
+ molecule=5
+ nres_molec(molecule)=nres_molec(molecule)+1
+ print *,"HERE",nres_molec(molecule)
+ res=res(2:3)//' '
+ itype(ires,molecule)=rescode(ires,res,0,molecule)
+ read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
+ endif
+ endif !atom
enddo
10 write (iout,'(a,i5)') ' Number of residues found: ',ires
if (ires.eq.0) return
! Calculate dummy residue coordinates inside the "chain" of a multichain
! system
nres=ires
+ if (((ires_old.ne.ires).and.(molecule.ne.5)) &
+ ) &
+ nres_molec(molecule)=nres_molec(molecule)-2
+ print *,'I have',nres, nres_molec(:)
+
+ do k=1,4 ! ions are without dummy
+ if (nres_molec(k).eq.0) cycle
do i=2,nres-1
-! write (iout,*) i,itype(i)
- if (itype(i).eq.ntyp1) then
-! 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
+! write (iout,*) i,itype(i,1)
+! if (itype(i,1).eq.ntyp1) then
+! write (iout,*) "dummy",i,itype(i,1)
+! 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
! c(j,i)=(c(j,i-1)+c(j,i+1))/2
- dc(j,i)=c(j,i)
- enddo
- endif
+! dc(j,i)=c(j,i)
+! enddo
+! endif
+ if (itype(i,k).eq.ntyp1_molec(k)) then
+ if (itype(i+1,k).eq.ntyp1_molec(k)) then
+ if (itype(i+2,k).eq.0) then
+! print *,"masz sieczke"
+ do j=1,5
+ if (itype(i+2,j).ne.0) then
+ itype(i+1,k)=0
+ itype(i+1,j)=ntyp1_molec(j)
+ nres_molec(k)=nres_molec(k)-1
+ nres_molec(j)=nres_molec(j)+1
+ go to 3331
+ endif
+ enddo
+ 3331 continue
+ endif
+! 16/01/2014 by Adasko: Adding to dummy atoms in the chain
+! first is connected prevous chain (itype(i+1,1).eq.ntyp1)=true
+! second dummy atom is conected to next chain itype(i+1,1).eq.ntyp1=false
+! if (unres_pdb) then
+! 2/15/2013 by Adam: corrected insertion of the last dummy residue
+! print *,i,'tu dochodze'
+! call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
+! if (fail) then
+! e2(1)=0.0d0
+! e2(2)=1.0d0
+! e2(3)=0.0d0
+! endif !fail
+! print *,i,'a tu?'
+! do j=1,3
+! c(j,i)=c(j,i-1)-1.9d0*e2(j)
+! enddo
+! else !unres_pdb
+ do j=1,3
+ dcj=(c(j,i-2)-c(j,i-3))/2.0
+ if (dcj.eq.0) dcj=1.23591524223
+ c(j,i)=c(j,i-1)+dcj
+ c(j,nres+i)=c(j,i)
+ enddo
+! endif !unres_pdb
+ else !itype(i+1,1).eq.ntyp1
+! if (unres_pdb) then
+! 2/15/2013 by Adam: corrected insertion of the first dummy residue
+! call refsys(i+1,i+2,i+3,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,i)=c(j,i+1)-1.9d0*e2(j)
+ enddo
+! else !unres_pdb
+ do j=1,3
+ dcj=(c(j,i+3)-c(j,i+2))/2.0
+ if (dcj.eq.0) dcj=1.23591524223
+ c(j,i)=c(j,i+1)-dcj
+ c(j,nres+i)=c(j,i)
+ enddo
+! endif !unres_pdb
+ endif !itype(i+1,1).eq.ntyp1
+ endif !itype.eq.ntyp1
+
+ enddo
enddo
! Calculate the CM of the last side chain.
if (iii.gt.0) then
! nres=ires
nsup=nres
nstart_sup=1
- if (itype(nres).ne.10) then
+! print *,"molecule",molecule
+ if ((itype(nres,1).ne.10)) then
nres=nres+1
- itype(nres)=ntyp1
- if (unres_pdb) then
+ if (molecule.eq.5) molecule=molecprev
+ itype(nres,molecule)=ntyp1_molec(molecule)
+ nres_molec(molecule)=nres_molec(molecule)+1
+! if (unres_pdb) then
! 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
+! 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)-1.9d0*e2(j)
+! enddo
+! else
do j=1,3
- dcj=c(j,nres-2)-c(j,nres-3)
+ dcj=(c(j,nres-2)-c(j,nres-3))/2.0
c(j,nres)=c(j,nres-1)+dcj
c(j,2*nres)=c(j,nres)
enddo
- endif
+! endif
endif
+! print *,'I have',nres, nres_molec(:)
+
!el kontrola nres w pliku inputowym WHAM-a w porownaniu z wartoscia wczytana z pliku pdb
#ifdef WHAM_RUN
if (nres.ne.nres0) then
c(j,nres+1)=c(j,1)
c(j,2*nres)=c(j,nres)
enddo
- if (itype(1).eq.ntyp1) then
+
+ if (itype(1,1).eq.ntyp1) then
nsup=nsup-1
nstart_sup=2
if (unres_pdb) then
e2(3)=0.0d0
endif
do j=1,3
- c(j,1)=c(j,2)-3.8d0*e2(j)
+ c(j,1)=c(j,2)-1.9d0*e2(j)
enddo
else
do j=1,3
- dcj=c(j,4)-c(j,3)
+ dcj=(c(j,4)-c(j,3))/2.0
c(j,1)=c(j,2)-dcj
c(j,nres+1)=c(j,1)
enddo
endif
endif
+! First lets assign correct dummy to correct type of chain
+! 1) First residue
+ if (itype(1,1).eq.ntyp1) then
+ if (itype(2,1).eq.0) then
+ do j=2,5
+ if (itype(2,j).ne.0) then
+ itype(1,1)=0
+ itype(1,j)=ntyp1_molec(j)
+ nres_molec(1)=nres_molec(1)-1
+ nres_molec(j)=nres_molec(j)+1
+ go to 3231
+ endif
+ enddo
+3231 continue
+ endif
+ endif
+ print *,'I have',nres, nres_molec(:)
+
! Copy the coordinates to reference coordinates
! do i=1,2*nres
! do j=1,3
if (lprn) then
write (iout,'(/a)') &
"Cartesian coordinates of the reference structure"
- write (iout,'(a,3(3x,a5),5x,3(3x,a5))') &
+ write (iout,'(a,16x,3(3x,a5),5x,3(3x,a5))') &
"Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
do ires=1,nres
- write (iout,'(a3,1x,i3,3f8.3,5x,3f8.3)') &
- restyp(itype(ires)),ires,(c(j,ires),j=1,3),&
+ write (iout,'(5(a3,1x),i5,3f8.3,5x,3f8.3)') &
+ (restyp(itype(ires,j),j),j=1,5),ires,(c(j,ires),j=1,3),&
(c(j,ires+nres),j=1,3)
enddo
endif
write (iout,'(a)') &
"Backbone and SC coordinates as read from the PDB"
do ires=1,nres
- write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)') &
- ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),&
+ write (iout,'(i5,i3,2x,a,3f8.3,5x,3f8.3)') &
+ ires,itype(ires,1),restyp(itype(ires,1),1),(c(j,ires),j=1,3),&
(c(j,nres+ires),j=1,3)
enddo
endif
+! NOW LETS ROCK! SORTING
+ allocate(c_temporary(3,2*nres))
+ allocate(itype_temporary(nres,5))
+ if (.not.allocated(molnum)) allocate(molnum(nres+1))
+ if (.not.allocated(istype)) write(iout,*) &
+ "SOMETHING WRONG WITH ISTYTPE"
+ allocate(istype_temp(nres))
+ itype_temporary(:,:)=0
+ seqalingbegin=1
+ do k=1,5
+ do i=1,nres
+ if (itype(i,k).ne.0) then
+ do j=1,3
+ c_temporary(j,seqalingbegin)=c(j,i)
+ c_temporary(j,seqalingbegin+nres)=c(j,i+nres)
+
+ enddo
+ itype_temporary(seqalingbegin,k)=itype(i,k)
+ print *,i,k,itype(i,k),itype_temporary(seqalingbegin,k),seqalingbegin
+ istype_temp(seqalingbegin)=istype(i)
+ molnum(seqalingbegin)=k
+ seqalingbegin=seqalingbegin+1
+ endif
+ enddo
+ enddo
+ do i=1,2*nres
+ do j=1,3
+ c(j,i)=c_temporary(j,i)
+ enddo
+ enddo
+ do k=1,5
+ do i=1,nres
+ itype(i,k)=itype_temporary(i,k)
+ istype(i)=istype_temp(i)
+ enddo
+ enddo
+! if (itype(1,1).eq.ntyp1) then
+! nsup=nsup-1
+! nstart_sup=2
+! if (unres_pdb) then
+! 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)-1.9d0*e2(j)
+! enddo
+! else
+! do j=1,3
+! dcj=(c(j,4)-c(j,3))/2.0
+! c(j,1)=c(j,2)-dcj
+! c(j,nres+1)=c(j,1)
+! enddo
+! endif
+! endif
+
+ if (lprn) then
+ write (iout,'(/a)') &
+ "Cartesian coordinates of the reference structure after sorting"
+ write (iout,'(a,16x,3(3x,a5),5x,3(3x,a5))') &
+ "Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
+ do ires=1,nres
+ write (iout,'(5(a3,1x),i5,3f8.3,5x,3f8.3)') &
+ (restyp(itype(ires,j),j),j=1,5),ires,(c(j,ires),j=1,3),&
+ (c(j,ires+nres),j=1,3)
+ enddo
+ endif
+! print *,seqalingbegin,nres
if(.not.allocated(vbld)) then
allocate(vbld(2*nres))
do i=1,2*nres
kkk=1
lll=0
cou=1
+ write (iout,*) "symetr", symetr
do i=1,nres
lll=lll+1
-!c write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
+! write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
if (i.gt.1) then
- if ((itype(i-1).eq.ntyp1).and.(i.gt.2)) then
+ if ((itype(i-1,1).eq.ntyp1).and.(i.gt.2)) then
chain_length=lll-1
kkk=kkk+1
! write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
! write (iout,*) "spraw lancuchy",chain_length,symetr
! do i=1,4
! do kkk=1,chain_length
-! write (iout,*) itype(kkk),(chain_rep(j,kkk,i), j=1,3)
+! write (iout,*) itype(kkk,1),(chain_rep(j,kkk,i), j=1,3)
! enddo
! enddo
! enddiagnostic
! makes copy of chains
write (iout,*) "symetr", symetr
+ do j=1,3
+ dc(j,0)=c(j,1)
+ enddo
if (symetr.gt.1) then
call permut(symetr)
cou=0
do kkk=1,symetr
icha=tabperm(i,kkk)
-! write (iout,*) i,icha
+ write (iout,*) i,icha
do lll=1,chain_length
cou=cou+1
if (cou.le.nres) then
kupa=mod(lll,chain_length)
iprzes=(kkk-1)*chain_length+lll
if (kupa.eq.0) kupa=chain_length
-! write (iout,*) "kupa", kupa
+ write (iout,*) "kupa", kupa
cref(j,iprzes,i)=chain_rep(j,kupa,icha)
cref(j,iprzes+nres,i)=chain_rep(j,kupa+nres,icha)
enddo
do kkk=1,nperm
write (iout,*) "nowa struktura", nperm
do i=1,nres
- write (iout,110) restyp(itype(i)),i,cref(1,i,kkk),&
+ write (iout,110) restyp(itype(i,1),1),i,cref(1,i,kkk),&
cref(2,i,kkk),&
cref(3,i,kkk),cref(1,nres+i,kkk),&
cref(2,nres+i,kkk),cref(3,nres+i,kkk)
enddo
- 100 format (//' alpha-carbon coordinates ',&
+ 100 format (//' alpha-carbon coordinates ',&
' centroid coordinates'/ &
' ', 6X,'X',11X,'Y',11X,'Z', &
10X,'X',11X,'Y',11X,'Z')
- 110 format (a,'(',i3,')',6f12.5)
+ 110 format (a,'(',i5,')',6f12.5)
enddo
!c enddiag
character(len=640) :: controlcard
real(kind=8) :: seed,rmsdbc,rmsdbc1max,rmsdbcm,drms,timem!,&
-
+ integer i
nglob_csa=0
eglob_csa=1d99
timem=timlim
modecalc=0
call reada(controlcard,"T_BATH",t_bath,300.0d0)
+!C SHIELD keyword sets if the shielding effect of side-chains is used
+!C 0 denots no shielding is used all peptide are equally despite the
+!C solvent accesible area
+!C 1 the newly introduced function
+!C 2 reseved for further possible developement
+ call readi(controlcard,'SHIELD',shield_mode,0)
+!C if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
+ write(iout,*) "shield_mode",shield_mode
+!C Varibles set size of box
+ with_theta_constr = index(controlcard,"WITH_THETA_CONSTR").gt.0
+ protein=index(controlcard,"PROTEIN").gt.0
+ ions=index(controlcard,"IONS").gt.0
+ nucleic=index(controlcard,"NUCLEIC").gt.0
+ write (iout,*) "with_theta_constr ",with_theta_constr
+ AFMlog=(index(controlcard,'AFM'))
+ selfguide=(index(controlcard,'SELFGUIDE'))
+ print *,'AFMlog',AFMlog,selfguide,"KUPA"
+ call readi(controlcard,'GENCONSTR',genconstr,0)
+ call reada(controlcard,'BOXX',boxxsize,100.0d0)
+ call reada(controlcard,'BOXY',boxysize,100.0d0)
+ call reada(controlcard,'BOXZ',boxzsize,100.0d0)
+ call readi(controlcard,'TUBEMOD',tubemode,0)
+ print *,"SCELE",scelemode
+ call readi(controlcard,"SCELEMODE",scelemode,0)
+ print *,"SCELE",scelemode
+
+! elemode = 0 is orignal UNRES electrostatics
+! elemode = 1 is "Momo" potentials in progress
+! elemode = 2 is in development EVALD
+ write (iout,*) TUBEmode,"TUBEMODE"
+ if (TUBEmode.gt.0) then
+ call reada(controlcard,"XTUBE",tubecenter(1),0.0d0)
+ call reada(controlcard,"YTUBE",tubecenter(2),0.0d0)
+ call reada(controlcard,"ZTUBE",tubecenter(3),0.0d0)
+ call reada(controlcard,"RTUBE",tubeR0,0.0d0)
+ call reada(controlcard,"TUBETOP",bordtubetop,boxzsize)
+ call reada(controlcard,"TUBEBOT",bordtubebot,0.0d0)
+ call reada(controlcard,"TUBEBUF",tubebufthick,1.0d0)
+ buftubebot=bordtubebot+tubebufthick
+ buftubetop=bordtubetop-tubebufthick
+ endif
+
+! CUTOFFF ON ELECTROSTATICS
+ call reada(controlcard,"R_CUT_ELE",r_cut_ele,15.0d0)
+ call reada(controlcard,"LAMBDA_ELE",rlamb_ele,0.3d0)
+ write(iout,*) "R_CUT_ELE=",r_cut_ele
+! Lipidic parameters
+ call reada(controlcard,"LIPTHICK",lipthick,0.0d0)
+ call reada(controlcard,"LIPAQBUF",lipbufthick,0.0d0)
+ if (lipthick.gt.0.0d0) then
+ bordliptop=(boxzsize+lipthick)/2.0
+ bordlipbot=bordliptop-lipthick
+ if ((bordliptop.gt.boxzsize).or.(bordlipbot.lt.0.0)) &
+ write(iout,*) "WARNING WRONG SIZE OF LIPIDIC PHASE"
+ buflipbot=bordlipbot+lipbufthick
+ bufliptop=bordliptop-lipbufthick
+ if ((lipbufthick*2.0d0).gt.lipthick) &
+ write(iout,*) "WARNING WRONG SIZE OF LIP AQ BUF"
+ endif !lipthick.gt.0
+ write(iout,*) "bordliptop=",bordliptop
+ write(iout,*) "bordlipbot=",bordlipbot
+ write(iout,*) "bufliptop=",bufliptop
+ write(iout,*) "buflipbot=",buflipbot
+ write (iout,*) "SHIELD MODE",shield_mode
+
+!C-------------------------
minim=(index(controlcard,'MINIMIZE').gt.0)
dccart=(index(controlcard,'CART').gt.0)
overlapsc=(index(controlcard,'OVERLAP').gt.0)
if(me.eq.king.or..not.out1file) &
write (iout,'(2a)') diagmeth(kdiag),&
' routine used to diagonalize matrices.'
+ if (shield_mode.gt.0) then
+ pi=4.0D0*datan(1.0D0)
+!C VSolvSphere the volume of solving sphere
+ print *,pi,"pi"
+!C rpp(1,1) is the energy r0 for peptide group contact and will be used for it
+!C there will be no distinction between proline peptide group and normal peptide
+!C group in case of shielding parameters
+ VSolvSphere=4.0/3.0*pi*(4.50d0)**3
+ VSolvSphere_div=VSolvSphere-4.0/3.0*pi*(4.50/2.0)**3
+ write (iout,*) VSolvSphere,VSolvSphere_div
+!C long axis of side chain
+! do i=1,ntyp
+! long_r_sidechain(i)=vbldsc0(1,i)
+! short_r_sidechain(i)=sigma0(i)
+! write(iout,*) "parame for long and short axis",i,vbldsc0(1,i),&
+! sigma0(i)
+! enddo
+ buff_shield=1.0d0
+ endif
return
end subroutine read_control
!-----------------------------------------------------------------------------
! character(len=80) :: ucase
character(len=320) :: controlcard
!el local variables
- integer :: i
+ integer :: i,j
real(kind=8) :: eta
call card_concat(controlcard,.true.)
large = index(controlcard,"LARGE").gt.0
print_compon = index(controlcard,"PRINT_COMPON").gt.0
rattle = index(controlcard,"RATTLE").gt.0
+ preminim=(index(controlcard,'PREMINIM').gt.0)
+ write (iout,*) "PREMINIM ",preminim
+ dccart=(index(controlcard,'CART').gt.0)
+ if (preminim) call read_minim
! if performing umbrella sampling, fragments constrained are read from the fragment file
nset=0
if(usampl) then
if(me.eq.king.or..not.out1file) &
write(iout,'(a60,f10.5)')"Eta of the solvent in natural units:",&
eta
- gamp=scal_fric*(pstok+rwat)*eta
- stdfp=dsqrt(2*Rb*t_bath/d_time)
- allocate(gamsc(ntyp1),stdfsc(ntyp1)) !(ntyp1)
+! allocate(gamp
+ do j=1,5 !types of molecules
+ gamp(j)=scal_fric*(pstok(j)+rwat)*eta
+ stdfp(j)=dsqrt(2*Rb*t_bath/d_time)
+ enddo
+ allocate(gamsc(ntyp1,5),stdfsc(ntyp1,5)) !(ntyp1)
+ do j=1,5 !types of molecules
do i=1,ntyp
- gamsc(i)=scal_fric*(restok(i)+rwat)*eta
- stdfsc(i)=dsqrt(2*Rb*t_bath/d_time)
+ gamsc(i,j)=scal_fric*(restok(i,j)+rwat)*eta
+ stdfsc(i,j)=dsqrt(2*Rb*t_bath/d_time)
enddo
+ enddo
+
if(me.eq.king.or..not.out1file)then
write (iout,'(/2a/)') &
"Radii of site types and friction coefficients and std's of",&
" stochastic forces of fully exposed sites"
- write (iout,'(a5,f5.2,2f10.5)')'p',pstok,gamp,stdfp*dsqrt(gamp)
+ write (iout,'(a5,f5.2,2f10.5)')'p',pstok,gamp(1),stdfp*dsqrt(gamp(1))
do i=1,ntyp
- write (iout,'(a5,f5.2,2f10.5)') restyp(i),restok(i),&
- gamsc(i),stdfsc(i)*dsqrt(gamsc(i))
+ write (iout,'(a5,f5.2,2f10.5)') restyp(i,1),restok(i,1),&
+ gamsc(i,1),stdfsc(i,1)*dsqrt(gamsc(i,1))
enddo
endif
else if (tbf) then
!-----------------------------------------------------------------------------
subroutine openunits
- use energy_data, only: usampl
+ use MD_data, only: usampl
use csa_data
use MPI_data
use control_data, only:out1file
! Get parameter filenames and open the parameter files.
call getenv_loc('BONDPAR',bondname)
open (ibond,file=bondname,status='old',readonly,shared)
+ call getenv_loc('BONDPAR_NUCL',bondname_nucl)
+ open (ibond_nucl,file=bondname_nucl,status='old',readonly,shared)
call getenv_loc('THETPAR',thetname)
open (ithep,file=thetname,status='old',readonly,shared)
call getenv_loc('ROTPAR',rotname)
open (ielep,file=elename,status='old',readonly,shared)
call getenv_loc('SIDEPAR',sidename)
open (isidep,file=sidename,status='old',readonly,shared)
+
+ call getenv_loc('THETPAR_NUCL',thetname_nucl)
+ open (ithep_nucl,file=thetname_nucl,status='old',readonly,shared)
+ call getenv_loc('ROTPAR_NUCL',rotname_nucl)
+ open (irotam_nucl,file=rotname_nucl,status='old',readonly,shared)
+ call getenv_loc('TORPAR_NUCL',torname_nucl)
+ open (itorp_nucl,file=torname_nucl,status='old',readonly,shared)
+ call getenv_loc('TORDPAR_NUCL',tordname_nucl)
+ open (itordp_nucl,file=tordname_nucl,status='old',readonly,shared)
+ call getenv_loc('SIDEPAR_NUCL',sidename_nucl)
+ open (isidep_nucl,file=sidename_nucl,status='old',readonly,shared)
+
+
#elif (defined CRAY) || (defined AIX)
open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old',&
action='read')
! Get parameter filenames and open the parameter files.
call getenv_loc('BONDPAR',bondname)
open (ibond,file=bondname,status='old',action='read')
+ call getenv_loc('BONDPAR_NUCL',bondname_nucl)
+ open (ibond_nucl,file=bondname_nucl,status='old',action='read')
+
! print *,"Processor",myrank," opened file IBOND"
call getenv_loc('THETPAR',thetname)
open (ithep,file=thetname,status='old',action='read')
! print *,"Processor",myrank," opened file IELEP"
call getenv_loc('SIDEPAR',sidename)
open (isidep,file=sidename,status='old',action='read')
+
+ call getenv_loc('THETPAR_NUCL',thetname_nucl)
+ open (ithep_nucl,file=thetname_nucl,status='old',action='read')
+ call getenv_loc('ROTPAR_NUCL',rotname_nucl)
+ open (irotam_nucl,file=rotname_nucl,status='old',action='read')
+ call getenv_loc('TORPAR_NUCL',torname_nucl)
+ open (itorp_nucl,file=torname_nucl,status='old',action='read')
+ call getenv_loc('TORDPAR_NUCL',tordname_nucl)
+ open (itordp_nucl,file=tordname_nucl,status='old',action='read')
+ call getenv_loc('SIDEPAR_NUCL',sidename_nucl)
+ open (isidep_nucl,file=sidename_nucl,status='old',action='read')
+
+ call getenv_loc('LIPTRANPAR',liptranname)
+ open (iliptranpar,file=liptranname,status='old',action='read')
+ call getenv_loc('TUBEPAR',tubename)
+ open (itube,file=tubename,status='old',action='read')
+ call getenv_loc('IONPAR',ionname)
+ open (iion,file=ionname,status='old',action='read')
+
! print *,"Processor",myrank," opened file ISIDEP"
! print *,"Processor",myrank," opened parameter files"
#elif (defined G77)
! Get parameter filenames and open the parameter files.
call getenv_loc('BONDPAR',bondname)
open (ibond,file=bondname,status='old')
+ call getenv_loc('BONDPAR_NUCL',bondname_nucl)
+ open (ibond_nucl,file=bondname_nucl,status='old')
+
call getenv_loc('THETPAR',thetname)
open (ithep,file=thetname,status='old')
call getenv_loc('ROTPAR',rotname)
open (ielep,file=elename,status='old')
call getenv_loc('SIDEPAR',sidename)
open (isidep,file=sidename,status='old')
+
+ open (ithep_nucl,file=thetname_nucl,status='old')
+ call getenv_loc('ROTPAR_NUCL',rotname_nucl)
+ open (irotam_nucl,file=rotname_nucl,status='old')
+ call getenv_loc('TORPAR_NUCL',torname_nucl)
+ open (itorp_nucl,file=torname_nucl,status='old')
+ call getenv_loc('TORDPAR_NUCL',tordname_nucl)
+ open (itordp_nucl,file=tordname_nucl,status='old')
+ call getenv_loc('SIDEPAR_NUCL',sidename_nucl)
+ open (isidep_nucl,file=sidename_nucl,status='old')
+
+ call getenv_loc('LIPTRANPAR',liptranname)
+ open (iliptranpar,file=liptranname,status='old')
+ call getenv_loc('TUBEPAR',tubename)
+ open (itube,file=tubename,status='old')
+ call getenv_loc('IONPAR',ionname)
+ open (iion,file=ionname,status='old')
#else
open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old',&
readonly)
! Get parameter filenames and open the parameter files.
call getenv_loc('BONDPAR',bondname)
open (ibond,file=bondname,status='old',action='read')
+ call getenv_loc('BONDPAR_NUCL',bondname_nucl)
+ open (ibond_nucl,file=bondname_nucl,status='old',action='read')
call getenv_loc('THETPAR',thetname)
open (ithep,file=thetname,status='old',action='read')
call getenv_loc('ROTPAR',rotname)
open (ielep,file=elename,status='old',readonly)
call getenv_loc('SIDEPAR',sidename)
open (isidep,file=sidename,status='old',readonly)
+
+ call getenv_loc('THETPAR_NUCL',thetname_nucl)
+ open (ithep_nucl,file=thetname_nucl,status='old',action='read')
+ call getenv_loc('ROTPAR_NUCL',rotname_nucl)
+ open (irotam_nucl,file=rotname_nucl,status='old',action='read')
+ call getenv_loc('TORPAR_NUCL',torname_nucl)
+ open (itorp_nucl,file=torname_nucl,status='old',action='read')
+ call getenv_loc('TORDPAR_NUCL',tordname_nucl)
+ open (itordp_nucl,file=tordname_nucl,status='old',action='read')
+ call getenv_loc('SIDEPAR_NUCL',sidename_nucl)
+ open (isidep_nucl,file=sidename_nucl,status='old',action='read')
+ call getenv_loc('SIDEPAR_SCBASE',sidename_scbase)
+ open (isidep_scbase,file=sidename_scbase,status='old',action='read')
+ call getenv_loc('PEPPAR_PEPBASE',pepname_pepbase)
+ open (isidep_pepbase,file=pepname_pepbase,status='old',action='read')
+ call getenv_loc('SCPAR_PHOSPH',pepname_scpho)
+ open (isidep_scpho,file=pepname_scpho,status='old',action='read')
+ call getenv_loc('PEPPAR_PHOSPH',pepname_peppho)
+ open (isidep_peppho,file=pepname_peppho,status='old',action='read')
+
+
+ call getenv_loc('LIPTRANPAR',liptranname)
+ open (iliptranpar,file=liptranname,status='old',action='read')
+ call getenv_loc('TUBEPAR',tubename)
+ open (itube,file=tubename,status='old',action='read')
+ call getenv_loc('IONPAR',ionname)
+ open (iion,file=ionname,status='old',action='read')
+
#ifndef CRYST_SC
call getenv_loc('ROTPARPDB',rotname_pdb)
open (irotam_pdb,file=rotname_pdb,status='old',action='read')
#endif
#endif
+ call getenv_loc('SCPPAR_NUCL',scpname_nucl)
+#if defined(WINIFL) || defined(WINPGI)
+ open (iscpp_nucl,file=scpname_nucl,status='old',readonly,shared)
+#elif (defined CRAY) || (defined AIX)
+ open (iscpp_nucl,file=scpname_nucl,status='old',action='read')
+#elif (defined G77)
+ open (iscpp_nucl,file=scpname_nucl,status='old')
+#else
+ open (iscpp_nucl,file=scpname_nucl,status='old',action='read')
+#endif
+
#ifndef OLDSCP
!
! 8/9/01 In the newest version SCp interaction constants are read from a file
subroutine readrst
use geometry_data, only: nres,dc
- use energy_data, only: usampl,iset
use MD_data
! implicit real*8 (a-h,o-z)
! include 'DIMENSIONS'
open(irest2,file=rest2name,status='unknown')
read(irest2,*) totT,EK,potE,totE,t_bath
+ totTafm=totT
! do i=1,2*nres
! AL 4/17/17: Now reading d_t(0,:) too
do i=0,2*nres
projects / unres4.git / blobdiff