2 10 4 4 6 4
-1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 2
+1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 2 3
Gppreg
4.58415E+01
1.05721E+03
- double precision ss_depth,ebr,d0cm,akcm,akth,akct,v1ss,v2ss,v3ss
+ double precision ss_depth,ebr,d0cm,akcm,akth,akct,v1ss,v2ss,v3ss,
+ &atriss,btriss,ctriss,dtriss
integer ns,nss,nfree,iss
common /sbridge/ ss_depth,ebr,d0cm,akcm,akth,akct,v1ss,v2ss,v3ss,
& ns,nss,nfree,iss(maxss)
logical dyn_ss,dyn_ss_mask
common /dyn_ssbond/ dyn_ssbond_ij(maxres,maxres),
& idssb(maxdim),jdssb(maxdim),
- & Ht,dyn_ss,dyn_ss_mask(maxres)
+ & Ht,dyn_ss,dyn_ss_mask(maxres),atriss,btriss,ctriss,dtriss
C Torsional constants of the rotation about virtual-bond dihedral angles
double precision v1,v2,vlor1,vlor2,vlor3,v0
integer itortyp,ntortyp,nterm,nlor,nterm_old
- common/torsion/v0(maxtor,maxtor),v1(maxterm,maxtor,maxtor),
- & v2(maxterm,maxtor,maxtor),vlor1(maxlor,maxtor,maxtor),
+ common/torsion/v0(-maxtor:maxtor,-maxtor:maxtor,2),
+ & v1(maxterm,-maxtor:maxtor,-maxtor:maxtor,2),
+ & v2(maxterm,-maxtor:maxtor,-maxtor:maxtor,2),
+ & vlor1(maxlor,-maxtor:maxtor,-maxtor:maxtor),
& vlor2(maxlor,maxtor,maxtor),vlor3(maxlor,maxtor,maxtor),
- & itortyp(ntyp),ntortyp,nterm(maxtor,maxtor),nlor(maxtor,maxtor)
+ & itortyp(-ntyp1:ntyp1),ntortyp,
+ & nterm(-maxtor:maxtor,-maxtor:maxtor,2),
+ & nlor(-maxtor:maxtor,-maxtor:maxtor,2)
& ,nterm_old
C 6/23/01 - constants for double torsionals
double precision v1c,v1s,v2c,v2s
integer ntermd_1,ntermd_2
- common /torsiond/ v1c(2,maxtermd_1,maxtor,maxtor,maxtor),
- & v1s(2,maxtermd_1,maxtor,maxtor,maxtor),
- & v2c(maxtermd_2,maxtermd_2,maxtor,maxtor,maxtor),
- & v2s(maxtermd_2,maxtermd_2,maxtor,maxtor,maxtor),
- & ntermd_1(maxtor,maxtor,maxtor),ntermd_2(maxtor,maxtor,maxtor)
+ common /torsiond/
+ &v1c(2,maxtermd_1,-maxtor:maxtor,-maxtor:maxtor,-maxtor:maxtor,2),
+ &v1s(2,maxtermd_1,-maxtor:maxtor,-maxtor:maxtor,-maxtor:maxtor,2),
+ &v2c(maxtermd_2,maxtermd_2,-maxtor:maxtor,-maxtor:maxtor,
+ & -maxtor:maxtor,2),
+ &v2s(maxtermd_2,maxtermd_2,-maxtor:maxtor,-maxtor:maxtor,
+ & -maxtor:maxtor,2),
+ & ntermd_1(-maxtor:maxtor,-maxtor:maxtor,-maxtor:maxtor,2),
+ & ntermd_2(-maxtor:maxtor,-maxtor:maxtor,-maxtor:maxtor,2)
C 9/18/99 - added Fourier coeffficients of the expansion of local energy
C surface
- double precision b1,b2,cc,dd,ee,ctilde,dtilde,b2tilde
+ double precision b1,b2,cc,dd,ee,ctilde,dtilde,b2tilde,b1tilde
integer nloctyp
- common/fourier/ b1(2,maxtor),b2(2,maxtor),cc(2,2,maxtor),
- & dd(2,2,maxtor),ee(2,2,maxtor),ctilde(2,2,maxtor),
- & dtilde(2,2,maxtor),b1tilde(2,maxtor),nloctyp
+ common/fourier/ b1(2,-maxtor:maxtor),b2(2,-maxtor:maxtor)
+ & ,cc(2,2,-maxtor:maxtor),
+ & dd(2,2,-maxtor:maxtor),ee(2,2,-maxtor:maxtor),
+ & ctilde(2,2,-maxtor:maxtor),
+ & dtilde(2,2,-maxtor:maxtor),b1tilde(2,-maxtor:maxtor),nloctyp
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=itype(j)
c dscj_inv=dsc_inv(itypj)
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))
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
-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))
phii1=phi(i+1)
gloci1=0.0D0
gloci2=0.0D0
- 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)
+ 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)
+ 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)
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
enddo
nlob(ntyp1)=0
dsc(ntyp1)=0.0D0
+ do iblock=1,2
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
+ v1(k,j,i,iblock)=0.0D0
+ v2(k,j,i,iblock)=0.0D0
enddo
enddo
enddo
+ enddo
do i=1,maxres
itype(i)=0
itel(i)=0
read (ithep,*,err=111,end=111) nthetyp,ntheterm,ntheterm2,
& ntheterm3,nsingle,ndouble
nntheterm=max0(ntheterm,ntheterm2,ntheterm3)
+C write(iout,*) "I am here",ntyp1
read (ithep,*,err=111,end=111) (ithetyp(i),i=1,ntyp1)
+C write(iout,*) "I am herew"
do i=-ntyp1,-1
ithetyp(i)=-ithetyp(-i)
enddo
C
read (itorp,*,end=113,err=113) ntortyp
read (itorp,*,end=113,err=113) (itortyp(i),i=1,ntyp)
-c write (iout,*) 'ntortyp',ntortyp
- do i=1,ntortyp
- do j=1,ntortyp
- read (itorp,*,end=113,err=113) nterm(i,j),nlor(i,j)
+ do iblock=1,2
+ do i=-ntyp,-1
+ itortyp(i)=-itortyp(-i)
+ enddo
+ 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)
v0ij=0.0d0
si=-1.0d0
- 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)
+ 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)
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)
+ do k=1,nlor(i,j,iblock)
read (itorp,*,end=113,err=113) kk,vlor1(k,i,j),
- & vlor2(k,i,j),vlor3(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 i=1,ntortyp
- do j=1,ntortyp
+ write (iout,'(/a/)') 'Torsional constants:'
+ do i=1,ntortyp
+ 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)
- write (iout,'(3(1pe15.5))')
+ 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
enddo
C
C 6/23/01 Read parameters for double torsionals
C
- do i=1,ntortyp
- do j=1,ntortyp
- do k=1,ntortyp
+C do i=1,ntortyp
+C do j=1,ntortyp
+C 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)',end=114,err=114) t1,t2,t3
c write (iout,*) "OK onelett",
c & i,j,k,t1,t2,t3
#endif
stop "Error in double torsional parameter file"
endif
- 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
+ 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
if (lprint) then
- write (iout,*)
+ write (iout,*)
write (iout,*) 'Constants for double torsionals'
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
C
read (isccor,*,end=1113,err=1113) nsccortyp
#ifdef SCCORPDB
+ write (iout,*) "Tu wchodze"
read (isccor,*,end=1113,err=1113) (isccortyp(i),i=1,ntyp)
do i=-ntyp,-1
isccortyp(i)=-isccortyp(-i)
enddo
iscprol=isccortyp(20)
-c write (iout,*) 'ntortyp',ntortyp
+C write (iout,*) 'ntortyp',ntortyp
maxinter=3
cc maxinter is maximum interaction sites
do l=1,maxinter
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,*,end=119,err=119) kk,v1sccor(k,l,i,j)
+ read (isccor,*,end=1113,err=1113) kk,v1sccor(k,l,i,j)
& ,v2sccor(k,l,i,j)
+c write(iout,*) "k=",kk
if (j.eq.iscprol) then
if (i.eq.isccortyp(10)) then
v1sccor(k,l,i,-j)=v1sccor(k,l,i,j)
endif
endif
endif
- read (isccor,*,end=1113,err=1113) kk,v1sccor(k,l,i,j)
- & ,v2sccor(k,l,i,j)
+C read (isccor,*,end=1113,err=1113) kk,v1sccor(k,l,i,j)
+C & ,v2sccor(k,l,i,j)
v0ijsccor=v0ijsccor+si*v1sccor(k,l,i,j)
v0ijsccor1=v0ijsccor+si*v1sccor(k,l,-i,j)
v0ijsccor2=v0ijsccor+si*v1sccor(k,l,i,-j)
enddo
close (isccor)
#else
+ write(iout,*) "a tu nie wchodze"
read (isccor,*,end=119,err=119) (isccortyp(i),i=1,ntyp)
c write (iout,*) 'ntortyp',ntortyp
maxinter=3
call reada(weightcard,"V2SS",v2ss,7.61d0)
call reada(weightcard,"V3SS",v3ss,13.7d0)
call reada(weightcard,"EBR",ebr,-5.50D0)
+ call reada(weightcard,"DTRISS",dtriss,1.0D0)
+ call reada(weightcard,"ATRISS",atriss,0.3D0)
+ call reada(weightcard,"BTRISS",btriss,0.02D0)
+ call reada(weightcard,"CTRISS",ctriss,1.0D0)
dyn_ss=(index(weightcard,'DYN_SS').gt.0)
do i=1,maxres
dyn_ss_mask(i)=.false.
c$$$ end
c$$$
c$$$C-----------------------------------------------------------------------------
+ subroutine triple_ssbond_ene(resi,resj,resk,eij)
+ include 'DIMENSIONS'
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.LOCAL'
+ include 'COMMON.INTERACT'
+ include 'COMMON.VAR'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CALC'
+#ifndef CLUST
+#ifndef WHAM
+ include 'COMMON.MD'
+#endif
+#endif
+
+c External functions
+ double precision h_base
+ external h_base
+
+c Input arguments
+ integer resi,resj,resk
+
+c Output arguments
+ double precision eij,eij1,eij2,eij3
+
+c Local variables
+ logical havebond
+c integer itypi,itypj,k,l
+ double precision rrij,ssd,deltat1,deltat2,deltat12,cosphi
+ double precision rrik,rrjk,rik,rjk,xi,xk,yi,yk,zi,zk,xij,yij,zij
+ double precision xik,yik,zik,xjk,yjk,zjk
+ double precision sig0ij,ljd,sig,fac,e1,e2
+ double precision dcosom1(3),dcosom2(3),ed
+ double precision pom1,pom2
+ double precision ljA,ljB,ljXs
+ double precision d_ljB(1:3)
+ double precision ssA,ssB,ssC,ssXs
+ double precision ssxm,ljxm,ssm,ljm
+ double precision d_ssxm(1:3),d_ljxm(1:3),d_ssm(1:3),d_ljm(1:3)
+
+ i=resi
+ j=resj
+ k=resk
+C write(iout,*) resi,resj,resk
+ itypi=itype(i)
+ dxi=dc_norm(1,nres+i)
+ dyi=dc_norm(2,nres+i)
+ dzi=dc_norm(3,nres+i)
+ dsci_inv=vbld_inv(i+nres)
+ xi=c(1,nres+i)
+ yi=c(2,nres+i)
+ zi=c(3,nres+i)
+
+ itypj=itype(j)
+ xj=c(1,nres+j)
+ yj=c(2,nres+j)
+ zj=c(3,nres+j)
+
+ dxj=dc_norm(1,nres+j)
+ dyj=dc_norm(2,nres+j)
+ dzj=dc_norm(3,nres+j)
+ dscj_inv=vbld_inv(j+nres)
+ itypk=itype(k)
+ xk=c(1,nres+k)
+ yk=c(2,nres+k)
+ zk=c(3,nres+k)
+
+ dxk=dc_norm(1,nres+k)
+ dyk=dc_norm(2,nres+k)
+ dzk=dc_norm(3,nres+k)
+ dscj_inv=vbld_inv(k+nres)
+ xij=xj-xi
+ xik=xk-xi
+ xjk=xk-xj
+ yij=yj-yi
+ yik=yk-yi
+ yjk=yk-yj
+ zij=zj-zi
+ zik=zk-zi
+ zjk=zk-zj
+ rrij=(xij*xij+yij*yij+zij*zij)
+ rij=dsqrt(rrij) ! sc_angular needs rij to really be the inverse
+ rrik=(xik*xik+yik*yik+zik*zik)
+ rik=dsqrt(rrik)
+ rrjk=(xjk*xjk+yjk*yjk+zjk*zjk)
+ rjk=dsqrt(rrjk)
+C there are three combination of distances for each trisulfide bonds
+C The first case the ith atom is the center
+C Energy function is E=d/(a*(x-y)**2+b*(x+y)**2+c) where x is first
+C distance y is second distance the a,b,c,d are parameters derived for
+C this problem d parameter was set as a penalty currenlty set to 1.
+ eij1=dtriss/(atriss*(rij-rik)**2+btriss*(rij+rik)**2+ctriss)
+C second case jth atom is center
+ eij2=dtriss/(atriss*(rij-rjk)**2+btriss*(rij+rjk)**2+ctriss)
+C the third case kth atom is the center
+ eij3=dtriss/(atriss*(rik-rjk)**2+btriss*(rik+rjk)**2+ctriss)
+C eij2=0.0
+C eij3=0.0
+C eij1=0.0
+ eij=eij1+eij2+eij3
+C write(iout,*)i,j,k,eij
+C The energy penalty calculated now time for the gradient part
+C derivative over rij
+ fac=-eij1**2/dtriss*(2.0*atriss*(rij-rik)+2.0*btriss*(rij+rik))
+ &-eij2**2/dtriss*(2.0*atriss*(rij-rjk)+2.0*btriss*(rij+rjk))
+ gg(1)=xij*fac/rij
+ gg(2)=yij*fac/rij
+ gg(3)=zij*fac/rij
+ do m=1,3
+ gvdwx(m,i)=gvdwx(m,i)-gg(m)
+ gvdwx(m,j)=gvdwx(m,j)+gg(m)
+ enddo
+ do l=1,3
+ gvdwc(l,i)=gvdwc(l,i)-gg(l)
+ gvdwc(l,j)=gvdwc(l,j)+gg(l)
+ enddo
+C now derivative over rik
+ fac=-eij1**2/dtriss*(-2.0*atriss*(rij-rik)+2.0*btriss*(rij+rik))
+ &-eij3**2/dtriss*(2.0*atriss*(rik-rjk)+2.0*btriss*(rik+rjk))
+ gg(1)=xik*fac/rik
+ gg(2)=yik*fac/rik
+ gg(3)=zik*fac/rik
+ do m=1,3
+ gvdwx(m,i)=gvdwx(m,i)-gg(m)
+ gvdwx(m,k)=gvdwx(m,k)+gg(m)
+ enddo
+ do l=1,3
+ gvdwc(l,i)=gvdwc(l,i)-gg(l)
+ gvdwc(l,k)=gvdwc(l,k)+gg(l)
+ enddo
+C now derivative over rjk
+ fac=-eij2**2/dtriss*(-2.0*atriss*(rij-rjk)+2.0*btriss*(rij+rjk))-
+ &eij3**2/dtriss*(-2.0*atriss*(rik-rjk)+2.0*btriss*(rik+rjk))
+ gg(1)=xjk*fac/rjk
+ gg(2)=yjk*fac/rjk
+ gg(3)=zjk*fac/rjk
+ do m=1,3
+ gvdwx(m,j)=gvdwx(m,j)-gg(m)
+ gvdwx(m,k)=gvdwx(m,k)+gg(m)
+ enddo
+ do l=1,3
+ gvdwc(l,j)=gvdwc(l,j)-gg(l)
+ gvdwc(l,k)=gvdwc(l,k)+gg(l)
+ enddo
+ return
+ end
double precision rri,xi,yi,zi,dxi,dyi,dzi,xmedi,ymedi,zmedi,
& xj,yj,zj,dxj,dyj,dzj,aaa,bbb,ael6i,ael3i,rrmij,rmij,r3ij,r6ij,
& vrmij,cosa,cosb,cosg,fac,ev1,ev2,fac3,fac4,evdwij,el1,el2,
- & eesij,ees,evdw,ene
+ & eesij,ees,evdw,ene, rij,zj_temp,xj_temp,yj_temp,
+ & sscale,sscagrad,dist_temp,xj_safe,yj_safe,zj_safe,dist_init
double precision elpp6c(2,2),elpp3c(2,2),ael6c(2,2),ael3c(2,2),
& appc(2,2),bppc(2,2)
double precision elcutoff,elecutoff_14
- integer ncont,icont(2,maxcont)
+ integer ncont,icont(2,maxcont),xshift,yshift,zshift,isubchap
double precision econt(maxcont)
*
* Load the constants of peptide bond - peptide bond interactions.
xmedi=xi+0.5*dxi
ymedi=yi+0.5*dyi
zmedi=zi+0.5*dzi
+ xmedi=mod(xmedi,boxxsize)
+ if (xmedi.lt.0) xmedi=xmedi+boxxsize
+ ymedi=mod(ymedi,boxysize)
+ if (ymedi.lt.0) ymedi=ymedi+boxysize
+ zmedi=mod(zmedi,boxzsize)
+ if (zmedi.lt.0) zmedi=zmedi+boxzsize
do 4 j=i+2,ien-1
ind=ind+1
iteli=itel(i)
dxj=c(1,j+1)-c(1,j)
dyj=c(2,j+1)-c(2,j)
dzj=c(3,j+1)-c(3,j)
- xj=c(1,j)+0.5*dxj-xmedi
- yj=c(2,j)+0.5*dyj-ymedi
- zj=c(3,j)+0.5*dzj-zmedi
+ xj=c(1,j)+0.5*dxj
+ yj=c(2,j)+0.5*dyj
+ zj=c(3,j)+0.5*dzj
+ xj=mod(xj,boxxsize)
+ if (xj.lt.0) xj=xj+boxxsize
+ yj=mod(yj,boxysize)
+ if (yj.lt.0) yj=yj+boxysize
+ zj=mod(zj,boxzsize)
+ if (zj.lt.0) zj=zj+boxzsize
+ dist_init=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2
+ xj_safe=xj
+ yj_safe=yj
+ zj_safe=zj
+ isubchap=0
+ do xshift=-1,1
+ do yshift=-1,1
+ do zshift=-1,1
+ xj=xj_safe+xshift*boxxsize
+ yj=yj_safe+yshift*boxysize
+ zj=zj_safe+zshift*boxzsize
+ dist_temp=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2
+ if(dist_temp.lt.dist_init) then
+ dist_init=dist_temp
+ xj_temp=xj
+ yj_temp=yj
+ zj_temp=zj
+ isubchap=1
+ endif
+ enddo
+ enddo
+ enddo
+ if (isubchap.eq.1) then
+ xj=xj_temp-xmedi
+ yj=yj_temp-ymedi
+ zj=zj_temp-zmedi
+ else
+ xj=xj_safe-xmedi
+ yj=yj_safe-ymedi
+ zj=zj_safe-zmedi
+ endif
+ rij=xj*xj+yj*yj+zj*zj
+ sss=sscale(sqrt(rij))
+ sssgrad=sscagrad(sqrt(rij))
rrmij=1.0/(xj*xj+yj*yj+zj*zj)
rmij=sqrt(rrmij)
r3ij=rrmij*rmij
econt(ncont)=eesij
endif
ees=ees+eesij
- evdw=evdw+evdwij
+ evdw=evdw+evdwij*sss
4 continue
1 continue
if (lprint) then
if (yj.lt.0) yj=yj+boxysize
zj=mod(zj,boxzsize)
if (zj.lt.0) zj=zj+boxzsize
- dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ dist_init=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2
xj_safe=xj
yj_safe=yj
zj_safe=zj
xj=xj_safe+xshift*boxxsize
yj=yj_safe+yshift*boxysize
zj=zj_safe+zshift*boxzsize
- dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ dist_temp=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2
if(dist_temp.lt.dist_init) then
dist_init=dist_temp
xj_temp=xj
yj=yj_safe-ymedi
zj=zj_safe-zmedi
endif
-
rij=xj*xj+yj*yj+zj*zj
sss=sscale(sqrt(rij))
sssgrad=sscagrad(sqrt(rij))
projects / unres.git / commitdiff