X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD-M%2Fenergy_p_new_barrier.F;h=b88ee576a2472ee07b7daa3bedfcf6a5ed11cf76;hb=ab83ff9e0b8281a0c667d3f9b64b006e5bd4fc9c;hp=e7199c4138e362ec742bd255bedb9045b03696a9;hpb=0d079e7aa471dbcbaed6a9cc98880425c0132437;p=unres.git

diff --git a/source/unres/src_MD-M/energy_p_new_barrier.F b/source/unres/src_MD-M/energy_p_new_barrier.F
index e7199c4..b88ee57 100644
--- a/source/unres/src_MD-M/energy_p_new_barrier.F
+++ b/source/unres/src_MD-M/energy_p_new_barrier.F
@@ -1420,6 +1420,9 @@ C
       include 'COMMON.CONTROL'
       include 'COMMON.SBRIDGE'
       logical lprn
+
+c      write(iout,*) "Jestem w egb(evdw)"
+
       evdw=0.0D0
 ccccc      energy_dec=.false.
 c     print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
@@ -1447,10 +1450,36 @@ 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))