X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Fcluster%2Fwham%2Fsrc-M%2Fenergy_p_new.F;h=05f78fee087e28df0c2971ce011fa44f9cccc0d2;hb=f7ed201184254bb7be2333857d07a78183752d45;hp=4814c1de0c0eecae4f9e1da00c6c76cf5d558af3;hpb=bc56c61e5f80e1552da5ce3332ab99c8351e67cf;p=unres.git

diff --git a/source/cluster/wham/src-M/energy_p_new.F b/source/cluster/wham/src-M/energy_p_new.F
index 4814c1d..05f78fe 100644
--- a/source/cluster/wham/src-M/energy_p_new.F
+++ b/source/cluster/wham/src-M/energy_p_new.F
@@ -107,7 +107,7 @@ c      write (iout,*) "ft(6)",fact(6)," evdw",evdw," evdw_t",evdw_t
       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
@@ -116,7 +116,7 @@ c      write (iout,*) "ft(6)",fact(6)," evdw",evdw," evdw_t",evdw_t
       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
@@ -232,6 +232,7 @@ c     &   +wsccor*fact(1)*gsccor_loc(i)
 c ROZNICA Z WHAMem
       enddo
       endif
+      if (dyn_ss) call dyn_set_nss
       return
       end
 C------------------------------------------------------------------------
@@ -763,6 +764,7 @@ C
       include 'COMMON.INTERACT'
       include 'COMMON.IOUNITS'
       include 'COMMON.CALC'
+      include 'COMMON.SBRIDGE'
       logical lprn
       common /srutu/icall
       integer icant
@@ -789,6 +791,38 @@ 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
+
+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
@@ -877,6 +911,7 @@ 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