X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD%2Freadrtns.F;h=10cde78274ba4d8d9e3ef5dc006b77eb1e84a9ec;hb=e123f68beb7954771018d0311468c68250b5f2d1;hp=4c1e4b9e9e3c85cab3805336973d714b432d05df;hpb=cc6bfed2a73175fb7329acdd60f3d89d9f25afbb;p=unres.git

diff --git a/source/unres/src_MD/readrtns.F b/source/unres/src_MD/readrtns.F
index 4c1e4b9..10cde78 100644
--- a/source/unres/src_MD/readrtns.F
+++ b/source/unres/src_MD/readrtns.F
@@ -860,12 +860,36 @@ C 12/1/95 Added weight for the multi-body term WCORR
       call reada(weightcard,"V2SS",v2ss,7.61d0)
       call reada(weightcard,"V3SS",v3ss,13.7d0)
       call reada(weightcard,"EBR",ebr,-5.50D0)
+      dyn_ss=(index(weightcard,'DYN_SS').gt.0)
+      do i=1,maxres
+        dyn_ss_mask(i)=.false.
+      enddo
+      do i=1,maxres-1
+        do j=i+1,maxres
+          dyn_ssbond_ij(i,j)=1.0d300
+        enddo
+      enddo
+      call reada(weightcard,"HT",Ht,0.0D0)
+      if (dyn_ss) then
+        ss_depth=ebr/wsc-0.25*eps(1,1)
+        Ht=Ht/wsc-0.25*eps(1,1)
+        akcm=akcm*wstrain/wsc
+        akth=akth*wstrain/wsc
+        akct=akct*wstrain/wsc
+        v1ss=v1ss*wstrain/wsc
+        v2ss=v2ss*wstrain/wsc
+        v3ss=v3ss*wstrain/wsc
+      else
+        ss_depth=ebr/wstrain-0.25*eps(1,1)*wsc/wstrain
+      endif
+
       if(me.eq.king.or..not.out1file) then
        write (iout,*) "Parameters of the SS-bond potential:"
        write (iout,*) "D0CM",d0cm," AKCM",akcm," AKTH",akth,
      & " AKCT",akct
        write (iout,*) "V1SS",v1ss," V2SS",v2ss," V3SS",v3ss
-       write (iout,*) "EBR",ebr
+       write (iout,*) "EBR",ebr," SS_DEPTH",ss_depth
+       write (iout,*)" HT",Ht
        print *,'indpdb=',indpdb,' pdbref=',pdbref
       endif
       if (indpdb.gt.0 .or. pdbref) then
@@ -893,6 +917,9 @@ c        print *,'Finished reading pdb data'
         call contact(.false.,ncont_ref,icont_ref,co)
 
         if (sideadd) then 
+C Following 2 lines for diagnostics; comment out if not needed
+         write (iout,*) "Before sideadd"
+         call intout
          if(me.eq.king.or..not.out1file)
      &    write(iout,*)'Adding sidechains'
          maxsi=1000
@@ -909,7 +936,12 @@ c        print *,'Finished reading pdb data'
      &              i,' after ',nsi,' trials'
           endif
          enddo
+C 10/03/12 Adam: Recalculate coordinates with new side chain positions
+         call chainbuild
         endif  
+C Following 2 lines for diagnostics; comment out if not needed
+        write (iout,*) "After sideadd"
+        call intout
       endif
       if (indpdb.eq.0) then
 C Read sequence if not taken from the pdb file.
@@ -930,8 +962,8 @@ C Assign initial virtual bond lengths
           vbld_inv(i)=vblinv
         enddo
         do i=2,nres-1
-          vbld(i+nres)=dsc(iabs(itype(i)))
-          vbld_inv(i+nres)=dsc_inv(iabs(itype(i)))
+          vbld(i+nres)=dsc(itype(i))
+          vbld_inv(i+nres)=dsc_inv(itype(i))
 c          write (iout,*) "i",i," itype",itype(i),
 c     &      " dsc",dsc(itype(i))," vbld",vbld(i),vbld(i+nres)
         enddo
@@ -1095,8 +1127,8 @@ czscore          call geom_to_var(nvar,coord_exp_zs(1,1))
 c        write (iout,*) "constr_dist",constr_dist,nstart_sup,nsup
       if (constr_dist.gt.0) then
         call read_dist_constr
-        call hpb_partition
       endif
+      if (nhpb.gt.0) call hpb_partition
 c      write (iout,*) "After read_dist_constr nhpb",nhpb
 c      call flush(iout)
       if (indpdb.eq.0 .and. modecalc.ne.2 .and. modecalc.ne.4
@@ -1151,7 +1183,6 @@ C initial geometry.
          enddo
          do i=2,nres-1
           omeg(i)=-120d0*deg2rad
-          if (itype(i).le.0) omeg(i)=-omeg(i)
          enddo
         else
           if(me.eq.king.or..not.out1file)
@@ -1218,6 +1249,21 @@ C Generate distance constraints, if the PDB structure is to be regularized.
         write (iout,'(/a,i3,a)') 
      &  'The chain contains',ns,' disulfide-bridging cysteines.'
         write (iout,'(20i4)') (iss(i),i=1,ns)
+       if (dyn_ss) then
+          write(iout,*)"Running with dynamic disulfide-bond formation"
+          do i=nss+1,nhpb
+            ihpb(i-nss)=ihpb(i)
+            jhpb(i-nss)=jhpb(i)
+            forcon(i-nss)=forcon(i)
+            dhpb(i-nss)=dhpb(i)
+          enddo
+          nhpb=nhpb-nss
+          nss=0
+          call hpb_partition
+          do i=1,ns
+            dyn_ss_mask(iss(i))=.true.
+          enddo
+       else
         write (iout,'(/a/)') 'Pre-formed links are:' 
 	do i=1,nss
 	  i1=ihpb(i)-nres
@@ -1230,6 +1276,7 @@ C Generate distance constraints, if the PDB structure is to be regularized.
      &    ebr,forcon(i)
 	enddo
 	write (iout,'(a)')
+       endif
       endif
       if (i2ndstr.gt.0) call secstrp2dihc
 c      call geom_to_var(nvar,x)
@@ -1293,10 +1340,12 @@ C Check whether the specified bridging residues are cystines.
       do i=1,ns
 	if (itype(iss(i)).ne.1) then
 	  if (me.eq.king.or..not.out1file) write (iout,'(2a,i3,a)') 
-     &   'Do you REALLY think that the residue ',restyp(iss(i)),i,
+     &   'Do you REALLY think that the residue ',
+     &    restyp(itype(iss(i))),i,
      &   ' can form a disulfide bridge?!!!'
 	  write (*,'(2a,i3,a)') 
-     &   'Do you REALLY think that the residue ',restyp(iss(i)),i,
+     &   'Do you REALLY think that the residue ',
+     &    restyp(itype(iss(i))),i,
      &   ' can form a disulfide bridge?!!!'
 #ifdef MPI
 	 call MPI_Finalize(MPI_COMM_WORLD,ierror)