Adding dyn_ss and triss potentials to src-M wham

[unres.git] / source / wham / src-M / molread_zs.F

diff --git a/source/wham/src-M/molread_zs.F b/source/wham/src-M/molread_zs.F
index 885c57b..4462f2d 100644 (file)
--- a/source/wham/src-M/molread_zs.F
+++ b/source/wham/src-M/molread_zs.F
@@ -52,21 +52,25 @@ C Convert sequence to numeric code
       write (iout,'(20i4)') (itype(i),i=1,nres)
       do i=1,nres-1
 #ifdef PROCOR
-        if (itype(i).eq.21 .or. itype(i+1).eq.21) then
+        if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) then
 #else
-        if (itype(i).eq.21) then
+        if (itype(i).eq.ntyp1) then
 #endif
           itel(i)=0
 #ifdef PROCOR
-        else if (itype(i+1).ne.20) then
+        else if (iabs(itype(i+1)).ne.20) then
 #else
-        else if (itype(i).ne.20) then
+        else if (iabs(itype(i)).ne.20) then
 #endif
           itel(i)=1
         else
           itel(i)=2
         endif
       enddo
+       write (iout,*) "ITEL"
+       do i=1,nres-1
+         write (iout,*) i,itype(i),itel(i)
+       enddo
       call read_bridge
 
       if (with_dihed_constr) then
@@ -91,8 +95,8 @@ C Convert sequence to numeric code
 
       nnt=1
       nct=nres
-      if (itype(1).eq.21) nnt=2
-      if (itype(nres).eq.21) nct=nct-1
+      if (itype(1).eq.ntyp1) nnt=2
+      if (itype(nres).eq.ntyp1) nct=nct-1
       write(iout,*) 'NNT=',NNT,' NCT=',NCT
       call setup_var
       call init_int_table
@@ -100,6 +104,9 @@ C Convert sequence to numeric code
         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"
+       else
         write (iout,'(/a/)') 'Pre-formed links are:' 
         do i=1,nss
          i1=ihpb(i)-nres
@@ -111,7 +118,22 @@ C Convert sequence to numeric code
      &    dhpb(i),ebr,forcon(i)
         enddo
       endif
+      endif
       write (iout,'(a)')
+      if (ns.gt.0.and.dyn_ss) then
+          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
+      endif
       return
       end
 c-----------------------------------------------------------------------------
@@ -150,10 +172,12 @@ C Check whether the specified bridging residues are cystines.
       do i=1,ns
        if (itype(iss(i)).ne.1) then
          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?!!!'
          stop
         endif