X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Fwham%2Fsrc-M%2Fenergy_p_new.F;h=1c3b3312986dbb56e6924197bbed94f5635f01af;hb=ddce4f732732bf7162e10539c3d94788be664317;hp=cac8518ddb97a2ee4fd112196b6958f1954e7c61;hpb=6f877b0a7b5b4f292dd52b2b447ececb7e469044;p=unres.git

diff --git a/source/wham/src-M/energy_p_new.F b/source/wham/src-M/energy_p_new.F
index cac8518..1c3b331 100644
--- a/source/wham/src-M/energy_p_new.F
+++ b/source/wham/src-M/energy_p_new.F
@@ -228,8 +228,11 @@ C
      &   +wturn3*fact(2)*gel_loc_turn3(i)
      &   +wturn6*fact(5)*gel_loc_turn6(i)
      &   +wel_loc*fact(2)*gel_loc_loc(i)
+c     &   +wsccor*fact(1)*gsccor_loc(i)
+c BYLA ROZNICA Z CLUSTER< OSTATNIA LINIA DODANA
       enddo
       endif
+      if (dyn_ss) call dyn_set_nss
       return
       end
 C------------------------------------------------------------------------
@@ -359,11 +362,14 @@ C
       integer icant
       external icant
 cd    print *,'Entering ELJ nnt=',nnt,' nct=',nct,' expon=',expon
+c ROZNICA z cluster
       do i=1,210
         do j=1,2
           eneps_temp(j,i)=0.0d0
         enddo
       enddo
+cROZNICA
+
       evdw=0.0D0
       evdw_t=0.0d0
       do i=iatsc_s,iatsc_e
@@ -397,8 +403,11 @@ c           write (iout,*)'i=',i,' j=',j,' itypi=',itypi,' itypj=',itypj
             e2=fac*bb(itypi,itypj)
             evdwij=e1+e2
             ij=icant(itypi,itypj)
+c ROZNICA z cluster
             eneps_temp(1,ij)=eneps_temp(1,ij)+e1/dabs(eps0ij)
             eneps_temp(2,ij)=eneps_temp(2,ij)+e2/eps0ij
+c
+
 cd          sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
 cd          epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
 cd          write (iout,'(2(a3,i3,2x),6(1pd12.4)/2(3(1pd12.4),5x)/)')
@@ -775,6 +784,7 @@ C
       include 'COMMON.ENEPS'
       include 'COMMON.IOUNITS'
       include 'COMMON.CALC'
+      include 'COMMON.SBRIDGE'
       logical lprn
       common /srutu/icall
       integer icant
@@ -806,6 +816,26 @@ C Calculate SC interaction energy.
 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
+            write (iout,'(a6,2i5,0pf7.3,a3,f10.3)')
+     &                        'evdw',i,j,evdwij,' ss',evdw
+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
+             write (iout,'(a6,2i5,0pf7.3,a3,f10.3)')
+     &                        'evdw',i,j,evdwij,'tss',evdw
+              endif!dyn_ss_mask(k)
+             enddo! k
+            ELSE
             ind=ind+1
             itypj=iabs(itype(j))
             if (itypj.eq.ntyp1) cycle
@@ -899,6 +929,7 @@ C Calculate the radial part of the gradient
 C Calculate angular part of the gradient.
             call sc_grad
             endif
+            ENDIF    ! dyn_ss            
           enddo      ! j
         enddo        ! iint
       enddo          ! i
@@ -2935,10 +2966,15 @@ C iii and jjj point to the residues for which the distance is assigned.
         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. 
+C        if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and. 
+C     & iabs(itype(jjj)).eq.1) then
+
+       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
+           endif
         else
 C Calculate the distance between the two points and its difference from the
 C target distance.
@@ -4622,6 +4658,7 @@ c   3 = SC...Ca...Ca...SCi
            esccor=esccor+v1ij*cosphi+v2ij*sinphi
            gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
          enddo
+      write (iout,*)"EBACK_SC_COR",esccor,i
 c      write (iout,*) "EBACK_SC_COR",i,v1ij*cosphi+v2ij*sinphi,intertyp,
 c     & nterm_sccor(isccori,isccori1),isccori,isccori1
 c        gloc_sc(intertyp,i-3,icg)=gloc_sc(intertyp,i-3,icg)+wsccor*gloci