etot=wsc*(evdw+fact(6)*evdw_t)+wscp*evdw2+welec*fact(1)*ees
& +wvdwpp*evdw1
& +wang*ebe+wtor*fact(1)*etors+wscloc*escloc
- & +wstrain*ehpb+nss*ebr+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5
+ & +wstrain*ehpb+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5
& +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4
& +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6
& +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d
etot=wsc*(evdw+fact(6)*evdw_t)+wscp*evdw2
& +welec*fact(1)*(ees+evdw1)
& +wang*ebe+wtor*fact(1)*etors+wscloc*escloc
- & +wstrain*ehpb+nss*ebr+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5
+ & +wstrain*ehpb+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5
& +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4
& +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6
& +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d
c ROZNICA Z WHAMem
enddo
endif
+ if (dyn_ss) call dyn_set_nss
return
end
C------------------------------------------------------------------------
include 'COMMON.INTERACT'
include 'COMMON.IOUNITS'
include 'COMMON.CALC'
+ include 'COMMON.SBRIDGE'
logical lprn
common /srutu/icall
integer icant
external icant
+ logical energy_dec /.true./
c print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
evdw_t=0.0d0
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
+
+c write(iout,*) "PRZED ZWYKLE", evdwij
+ call dyn_ssbond_ene(i,j,evdwij)
+c write(iout,*) "PO ZWYKLE", 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
+
+c write(iout,*) "PRZED TRI", evdwij
+ evdwij_przed_tri=evdwij
+ call triple_ssbond_ene(i,j,k,evdwij)
+c if(evdwij_przed_tri.ne.evdwij) then
+c write (iout,*) "TRI:", evdwij, evdwij_przed_tri
+c endif
+
+c write(iout,*) "PO TRI", 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
ind=ind+1
itypj=iabs(itype(j))
if (itypj.eq.ntyp1) cycle
C Calculate angular part of the gradient.
call sc_grad
endif
+ ENDIF ! dyn_ss
enddo ! j
enddo ! iint
enddo ! i
endif
C 24/11/03 AL: SS bridges handled separately because of introducing a specific
C distance and angle dependent SS bond potential.
- if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and.
- & iabs(itype(jjj)).eq.1) then
+C if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and.
+C & iabs(itype(jjj)).eq.1) then
+C call ssbond_ene(iii,jjj,eij)
+C ehpb=ehpb+2*eij
+C else
+ if (.not.dyn_ss .and. i.le.nss) then
+ if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and.
+ & iabs(itype(jjj)).eq.1) then
call ssbond_ene(iii,jjj,eij)
ehpb=ehpb+2*eij
- else
+ endif !ii.gt.neres
+ else if (ii.gt.nres .and. jj.gt.nres) then
+c Restraints from contact prediction
+ dd=dist(ii,jj)
+ if (constr_dist.eq.11) then
+C ehpb=ehpb+fordepth(i)**4.0d0
+C & *rlornmr1(dd,dhpb(i),dhpb1(i),forcon(i))
+ ehpb=ehpb+fordepth(i)**4.0d0
+ & *rlornmr1(dd,dhpb(i),dhpb1(i),forcon(i))
+ fac=fordepth(i)**4.0d0
+ & *rlornmr1prim(dd,dhpb(i),dhpb1(i),forcon(i))/dd
+C write (iout,'(a6,2i5,3f8.3)') "edisl",ii,jj,
+C & ehpb,fordepth(i),dd
+C write(iout,*) ehpb,"atu?"
+C ehpb,"tu?"
+C fac=fordepth(i)**4.0d0
+C & *rlornmr1prim(dd,dhpb(i),dhpb1(i),forcon(i))/dd
+ else !constr_dist.eq.11
+ if (dhpb1(i).gt.0.0d0) then
+ ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd
+c write (iout,*) "beta nmr",
+c & dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ else !dhpb(i).gt.0.00
+
C Calculate the distance between the two points and its difference from the
C target distance.
dd=dist(ii,jj)
C Evaluate gradient.
C
fac=waga*rdis/dd
+ endif !dhpb(i).gt.0
+ endif
cd print *,'i=',i,' ii=',ii,' jj=',jj,' dhpb=',dhpb(i),' dd=',dd,
cd & ' waga=',waga,' fac=',fac
do j=1,3
ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j)
enddo
endif
+ else !ii.gt.nres
+C write(iout,*) "before"
+ dd=dist(ii,jj)
+C write(iout,*) "after",dd
+ if (constr_dist.eq.11) then
+ ehpb=ehpb+fordepth(i)**4.0d0
+ & *rlornmr1(dd,dhpb(i),dhpb1(i),forcon(i))
+ fac=fordepth(i)**4.0d0
+ & *rlornmr1prim(dd,dhpb(i),dhpb1(i),forcon(i))/dd
+C ehpb=ehpb+fordepth(i)**4*rlornmr1(dd,dhpb(i),dhpb1(i))
+C fac=fordepth(i)**4*rlornmr1prim(dd,dhpb(i),dhpb1(i))/dd
+C print *,ehpb,"tu?"
+C write(iout,*) ehpb,"btu?",
+C & dd,dhpb(i),dhpb1(i),fordepth(i),forcon(i)
+C write (iout,'(a6,2i5,3f8.3)') "edisl",ii,jj,
+C & ehpb,fordepth(i),dd
+ else
+ if (dhpb1(i).gt.0.0d0) then
+ ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd
+c write (iout,*) "alph nmr",
+c & dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ else
+ rdis=dd-dhpb(i)
+C Get the force constant corresponding to this distance.
+ waga=forcon(i)
+C Calculate the contribution to energy.
+ ehpb=ehpb+waga*rdis*rdis
+c write (iout,*) "alpha reg",dd,waga*rdis*rdis
+C
+C Evaluate gradient.
+C
+ fac=waga*rdis/dd
+ endif
+ endif
+ do j=1,3
+ ggg(j)=fac*(c(j,jj)-c(j,ii))
+ enddo
+cd print '(i3,3(1pe14.5))',i,(ggg(j),j=1,3)
+C If this is a SC-SC distance, we need to calculate the contributions to the
+C Cartesian gradient in the SC vectors (ghpbx).
+ if (iii.lt.ii) then
+ do j=1,3
+ ghpbx(j,iii)=ghpbx(j,iii)-ggg(j)
+ ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j)
+ enddo
+ endif
do j=iii,jjj-1
do k=1,3
ghpbc(k,j)=ghpbc(k,j)+ggg(k)
enddo
endif
enddo
- ehpb=0.5D0*ehpb
+ if (constr_dist.ne.11) ehpb=0.5D0*ehpb
return
end
C--------------------------------------------------------------------------
projects / unres.git / blobdiff