X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Fwham%2Fsrc%2Fmolread_zs.F;h=cdc6f454c6db3f13bf9d0a512b0a84ee91c26d72;hb=34d3ad3987785642be58fb2f26557d3314215577;hp=87a34953ecd4fd1559fb7dffbfe4e260c4f08629;hpb=24bbf0f3f06452c69bf4b69b4a9ba620e0260d7b;p=unres.git

diff --git a/source/wham/src/molread_zs.F b/source/wham/src/molread_zs.F
index 87a3495..cdc6f45 100644
--- a/source/wham/src/molread_zs.F
+++ b/source/wham/src/molread_zs.F
@@ -48,6 +48,19 @@ C Convert sequence to numeric code
       do i=1,nres
         itype(i)=rescode(i,sequence(i),iscode)
       enddo
+      if (itype(2).eq.10.and.itype(1).eq.ntyp1) then
+        write (iout,*)
+     &   "Glycine is the first full residue, initial dummy deleted"
+        do i=1,nres
+          itype(i)=itype(i+1)
+        enddo
+        nres=nres-1
+      endif
+      if (itype(nres-1).eq.10.and.itype(nres).eq.ntyp1) then
+        write (iout,*)
+     &   "Glycine is the last full residue, terminal dummy deleted"
+        nres=nres-1
+      endif
       write (iout,*) "Numeric code:"
       write (iout,'(20i4)') (itype(i),i=1,nres)
       do i=1,nres-1
@@ -96,6 +109,7 @@ C Convert sequence to numeric code
       write(iout,*) 'NNT=',NNT,' NCT=',NCT
 c Read distance restraints
       if (constr_dist.gt.0) then
+        if (refstr) call read_ref_structure(*11)
         call read_dist_constr
         call hpb_partition
       endif
@@ -119,6 +133,7 @@ c Read distance restraints
       endif
       write (iout,'(a)')
       return
+   11 stop "Error reading reference structure"
       end
 c-----------------------------------------------------------------------------
       logical function seq_comp(itypea,itypeb,length)
@@ -202,6 +217,25 @@ C bridging residues.
         enddo
       endif
       endif
+      if (ns.gt.0.and.dyn_ss) then
+C /06/28/2013 Adasko:ns is number of Cysteins bonded also called half of
+C the bond
+          do i=nss+1,nhpb
+C /06/28/2013 Adasko: nss number of full SS bonds
+            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.
+C /06/28/2013 Adasko: dyn_ss_mask which Cysteins can form disulfidebond
+c          write(iout,*) i,iss(i),dyn_ss_mask(iss(i)),"ATU"
+          enddo
+      endif
       return
       end
 c------------------------------------------------------------------------------