readpdb & fort.2 from unres
authorCezary Czaplewski <czarek@chem.univ.gda.pl>
Sat, 4 Apr 2020 22:59:40 +0000 (00:59 +0200)
committerCezary Czaplewski <czarek@chem.univ.gda.pl>
Sat, 4 Apr 2020 22:59:40 +0000 (00:59 +0200)
source/cluster/wham/src-HCD/readpdb.F
source/unres/src-HCD-5D/Makefile_MPICH_ifort-okeanos
source/unres/src-HCD-5D/readpdb-mult.F
source/unres/src-HCD-5D/rmscalc.F
source/wham/src-HCD/readpdb.F

index 2e73601..98e538e 100644 (file)
@@ -21,6 +21,7 @@ C geometry.
       character*80 card
       double precision sccor(3,20)
       integer rescode
+      integer iterter(maxres)
       efree_temp=0.0d0
       ibeg=1
       ishift1=0
@@ -34,53 +35,73 @@ c      write (2,*) "UNRES_PDB",unres_pdb
       nbfrag=0
       do
         read (ipdbin,'(a80)',end=10) card
-c        write (iout,'(a)') card
+!       write (iout,'(a)') card
         if (card(:5).eq.'HELIX') then
-         nhfrag=nhfrag+1
-         lsecondary=.true.
-         read(card(22:25),*) hfrag(1,nhfrag)
-         read(card(34:37),*) hfrag(2,nhfrag)
+          nhfrag=nhfrag+1
+          lsecondary=.true.
+          read(card(22:25),*) hfrag(1,nhfrag)
+          read(card(34:37),*) hfrag(2,nhfrag)
         endif
         if (card(:5).eq.'SHEET') then
-         nbfrag=nbfrag+1
-         lsecondary=.true.
-         read(card(24:26),*) bfrag(1,nbfrag)
-         read(card(35:37),*) bfrag(2,nbfrag)
-crc----------------------------------------
-crc  to be corrected !!!
-         bfrag(3,nbfrag)=bfrag(1,nbfrag)
-         bfrag(4,nbfrag)=bfrag(2,nbfrag)
-crc----------------------------------------
+          nbfrag=nbfrag+1
+          lsecondary=.true.
+          read(card(24:26),*) bfrag(1,nbfrag)
+          read(card(35:37),*) bfrag(2,nbfrag)
+!rc----------------------------------------
+!rc  to be corrected !!!
+          bfrag(3,nbfrag)=bfrag(1,nbfrag)
+          bfrag(4,nbfrag)=bfrag(2,nbfrag)
+!rc----------------------------------------
         endif
-        if (card(:3).eq.'END' .or. card(:3).eq.'TER') goto 10
-c Read free energy
+        if (card(:3).eq.'END') then
+          goto 10
+        else if (card(:3).eq.'TER') then
+! End current chain
+          ires_old=ires+2
+          itype(ires_old-1)=ntyp1
+          iterter(ires_old-1)=1
+          itype(ires_old)=ntyp1
+          ishift1=ishift1+1
+          ibeg=2
+!          write (iout,*) "Chain ended",ires,ishift,ires_old
+          if (unres_pdb) then
+            do j=1,3
+              dc(j,ires)=sccor(j,iii)
+            enddo
+          else
+            call sccenter(ires,iii,sccor)
+          endif
+c          iii=0
+        endif
+! Read free energy
         if (index(card,"FREE ENERGY").gt.0) read(card(35:),*) efree_temp
-C Fish out the ATOM cards.
+! Fish out the ATOM cards.
         if (index(card(1:4),'ATOM').gt.0) then  
           read (card(12:16),*) atom
-c          write (iout,*) "! ",atom," !",ires
-c          if (atom.eq.'CA' .or. atom.eq.'CH3') then
+c          write (2,'(a)') card
+!          write (iout,*) "! ",atom," !",ires
+!          if (atom.eq.'CA' .or. atom.eq.'CH3') then
           read (card(23:26),*) ires
           read (card(18:20),'(a3)') res
-c          write (iout,*) "ires",ires,ires-ishift+ishift1,
-c     &      " ires_old",ires_old
-c          write (iout,*) "ishift",ishift," ishift1",ishift1
-c          write (iout,*) "IRES",ires-ishift+ishift1,ires_old
+!          write (iout,*) "ires",ires,ires-ishift+ishift1,
+!     &      " ires_old",ires_old
+!          write (iout,*) "ishift",ishift," ishift1",ishift1
+!          write (iout,*) "IRES",ires-ishift+ishift1,ires_old
           if (ires-ishift+ishift1.ne.ires_old) then
-C Calculate the CM of the preceding residue.
-c            if (ibeg.eq.0) call sccenter(ires,iii,sccor)
+! Calculate the CM of the preceding residue.
+!            if (ibeg.eq.0) call sccenter(ires,iii,sccor)
             if (ibeg.eq.0) then
-c              write (iout,*) "Calculating sidechain center iii",iii
+!              write (iout,*) "Calculating sidechain center iii",iii
               if (unres_pdb) then
                 do j=1,3
-                  dc(j,ires)=sccor(j,iii)
+                  dc(j,ires+nres)=sccor(j,iii)
                 enddo
               else
                 call sccenter(ires_old,iii,sccor)
               endif
               iii=0
             endif
-C Start new residue.
+! Start new residue.
             if (res.eq.'Cl-' .or. res.eq.'Na+') then
               ires=ires_old
               cycle
@@ -93,9 +114,17 @@ c              write (iout,*) "BEG ires",ires
               endif
               ires=ires-ishift+ishift1
               ires_old=ires
-c              write (iout,*) "ishift",ishift," ires",ires,
-c     &         " ires_old",ires_old
-              ibeg=0          
+!              write (iout,*) "ishift",ishift," ires",ires,&
+!               " ires_old",ires_old
+              ibeg=0 
+            else if (ibeg.eq.2) then
+! Start a new chain
+              ishift=-ires_old+ires-1 !!!!!
+              ishift1=ishift1-1    !!!!!
+!              write (iout,*) "New chain started",ires,ishift,ishift1,"!"
+              ires=ires-ishift+ishift1
+              ires_old=ires
+              ibeg=0
             else
               ishift=ishift-(ires-ishift+ishift1-ires_old-1)
               ires=ires-ishift+ishift1
@@ -109,15 +138,15 @@ c     &         " ires_old",ires_old
           else
             ires=ires-ishift+ishift1
           endif
-c          write (iout,*) "ires_old",ires_old," ires",ires
+!          write (iout,*) "ires_old",ires_old," ires",ires
           if (card(27:27).eq."A" .or. card(27:27).eq."B") then
-c            ishift1=ishift1+1
+!            ishift1=ishift1+1
           endif
-c          write (2,*) "ires",ires," res ",res," ity",ity
+!          write (2,*) "ires",ires," res ",res!," ity"!,ity 
           if (atom.eq.'CA' .or. atom.eq.'CH3' .or. 
      &       res.eq.'NHE'.and.atom(:2).eq.'HN') then
             read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
-c            write (iout,*) "backbone ",atom 
+!            write (iout,*) "backbone ",atom
 #ifdef DEBUG
             write (iout,'(2i3,2x,a,3f8.3)') 
      &      ires,itype(ires),res,(c(j,ires),j=1,3)
@@ -126,19 +155,15 @@ c            write (iout,*) "backbone ",atom
             do j=1,3
               sccor(j,iii)=c(j,ires)
             enddo
-            if (ishift.ne.0) then
-              ires_ca=ires+ishift-ishift1
-            else
-              ires_ca=ires
-            endif
-c            write (*,*) card(23:27),ires,itype(ires)
-          else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and.
-     &             atom.ne.'N' .and. atom.ne.'C' .and.
-     &             atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and.
+c            write (2,*) card(23:27),ires,itype(ires),iii
+          else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and. 
+     &             atom.ne.'N' .and. atom.ne.'C' .and. 
+     &             atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and. 
      &             atom.ne.'OXT' .and. atom(:2).ne.'3H') then
-c            write (iout,*) "sidechain ",atom
+!            write (iout,*) "sidechain ",atom
             iii=iii+1
             read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
+c            write (2,*) "iii",iii
           endif
         endif
       enddo
@@ -474,22 +499,36 @@ c---------------------------------------------------------------------------
       end
 c---------------------------------------------------------------------------
       subroutine bond_regular
-      implicit real*8 (a-h,o-z)
-      include 'DIMENSIONS'   
+      implicit none
+      include 'DIMENSIONS'
       include 'COMMON.VAR'
-      include 'COMMON.LOCAL'      
-      include 'COMMON.CALC'
+      include 'COMMON.LOCAL'
       include 'COMMON.INTERACT'
       include 'COMMON.CHAIN'
+      integer i,i1,i2
       do i=1,nres-1
        vbld(i+1)=vbl
-       vbld_inv(i+1)=1.0d0/vbld(i+1)
-       vbld(i+1+nres)=dsc(itype(i+1))
-       vbld_inv(i+1+nres)=dsc_inv(itype(i+1))
+       vbld_inv(i+1)=vblinv
+       vbld(i+1+nres)=dsc(iabs(itype(i+1)))
+       vbld_inv(i+1+nres)=dsc_inv(iabs(itype(i+1)))
 c       print *,vbld(i+1),vbld(i+1+nres)
       enddo
+c Adam 2/26/20 Alter virtual bonds for non-blocking end groups of each chain
+      do i=1,nchain
+        i1=chain_border(1,i)
+        i2=chain_border(2,i)
+        if (i1.gt.1) then
+          vbld(i1)=vbld(i1)/2
+          vbld_inv(i1)=vbld_inv(i1)*2
+        endif
+        if (i2.lt.nres) then
+          vbld(i2+1)=vbld(i2+1)/2
+          vbld_inv(i2+1)=vbld_inv(i2+1)*2
+        endif
+      enddo
       return
       end
+c---------------------------------------------------------------------------
       subroutine readpdb_template(k)
 C Read the PDB file with gaps for read_constr_homology with read2sigma
 C and convert the peptide geometry into virtual-chain geometry.
index 9826556..ac97e59 100644 (file)
@@ -40,7 +40,7 @@ object = unres.o arcos.o cartprint.o chainbuild.o convert.o initialize_p.o \
         cart2intgrad.o checkder_p.o contact_cp econstr_local.o econstr_qlike.o \
        econstrq-PMF.o PMFprocess.o energy_p_new_barrier.o make_xx_list.o \
        energy_p_new-sep_barrier.o gradient_p.o minimize_p.o sumsld.o \
-        cored.o rmdd.o geomout.o readpdb.o int_from_cart.o regularize.o \
+        cored.o rmdd.o geomout.o readpdb-mult.o int_from_cart.o regularize.o \
        thread.o fitsq.o mcm.o \
         mc.o bond_move.o refsys.o check_sc_distr.o check_bond.o contact.o \
         eigen.o blas.o add.o entmcm.o minim_mcmf.o \
index 8fd1da8..9b99e64 100644 (file)
@@ -21,7 +21,7 @@ C geometry.
       integer rescode,iterter(maxres),cou
       logical fail
       integer i,j,iii,ires,ires_old,ishift,ishift1,ibeg
-      double precision dcj
+      double precision dcj,efree_temp
       bfac=0.0d0
       do i=1,maxres
          iterter(i)=0
@@ -33,103 +33,141 @@ C geometry.
       nbfrag=0
       do
         read (ipdbin,'(a80)',end=10) card
+!       write (iout,'(a)') card
         if (card(:5).eq.'HELIX') then
-         nhfrag=nhfrag+1
-         lsecondary=.true.
-         read(card(22:25),*) hfrag(1,nhfrag)
-         read(card(34:37),*) hfrag(2,nhfrag)
+          nhfrag=nhfrag+1
+          lsecondary=.true.
+          read(card(22:25),*) hfrag(1,nhfrag)
+          read(card(34:37),*) hfrag(2,nhfrag)
         endif
         if (card(:5).eq.'SHEET') then
-         nbfrag=nbfrag+1
-         lsecondary=.true.
-         read(card(24:26),*) bfrag(1,nbfrag)
-         read(card(35:37),*) bfrag(2,nbfrag)
-crc----------------------------------------
-crc  to be corrected !!!
-         bfrag(3,nbfrag)=bfrag(1,nbfrag)
-         bfrag(4,nbfrag)=bfrag(2,nbfrag)
-crc----------------------------------------
+          nbfrag=nbfrag+1
+          lsecondary=.true.
+          read(card(24:26),*) bfrag(1,nbfrag)
+          read(card(35:37),*) bfrag(2,nbfrag)
+!rc----------------------------------------
+!rc  to be corrected !!!
+          bfrag(3,nbfrag)=bfrag(1,nbfrag)
+          bfrag(4,nbfrag)=bfrag(2,nbfrag)
+!rc----------------------------------------
         endif
         if (card(:3).eq.'END') then
           goto 10
         else if (card(:3).eq.'TER') then
-C End current chain
+! End current chain
           ires_old=ires+2
-          itype(ires_old-1)=ntyp1 
+          itype(ires_old-1)=ntyp1
           iterter(ires_old-1)=1
           itype(ires_old)=ntyp1
-          iterter(ires_old)=1
+          ishift1=ishift1+1
           ibeg=2
-          write (iout,*) "Chain ended",ires,ishift,ires_old
+!          write (iout,*) "Chain ended",ires,ishift,ires_old
           if (unres_pdb) then
             do j=1,3
               dc(j,ires)=sccor(j,iii)
             enddo
-          else 
+          else
             call sccenter(ires,iii,sccor)
           endif
+c          iii=0
         endif
-C Fish out the ATOM cards.
-c        if (index(card(1:4),'ATOM').gt.0) then  
-c          read (card(14:16),'(a3)') atom
-c          if (atom.eq.'CA' .or. atom.eq.'CH3') then
-C Calculate the CM of the preceding residue.
-        read (card(23:26),*) ires
-        read (card(18:20),'(a3)') res
-        if (ires-ishift+ishift1.ne.ires_old) then
-          if (ibeg.eq.0) then
-            if (unres_pdb) then
-              do j=1,3
-                dc(j,ires+nres)=sccor(j,iii)
-              enddo
+! Read free energy
+        if (index(card,"FREE ENERGY").gt.0) read(card(35:),*) efree_temp
+! Fish out the ATOM cards.
+        if (index(card(1:4),'ATOM').gt.0) then  
+          read (card(12:16),*) atom
+c          write (2,'(a)') card
+!          write (iout,*) "! ",atom," !",ires
+!          if (atom.eq.'CA' .or. atom.eq.'CH3') then
+          read (card(23:26),*) ires
+          read (card(18:20),'(a3)') res
+!          write (iout,*) "ires",ires,ires-ishift+ishift1,
+!     &      " ires_old",ires_old
+!          write (iout,*) "ishift",ishift," ishift1",ishift1
+!          write (iout,*) "IRES",ires-ishift+ishift1,ires_old
+          if (ires-ishift+ishift1.ne.ires_old) then
+! Calculate the CM of the preceding residue.
+!            if (ibeg.eq.0) call sccenter(ires,iii,sccor)
+            if (ibeg.eq.0) then
+!              write (iout,*) "Calculating sidechain center iii",iii
+              if (unres_pdb) then
+                do j=1,3
+                  dc(j,ires+nres)=sccor(j,iii)
+                enddo
+              else
+                call sccenter(ires_old,iii,sccor)
+              endif
+              iii=0
+            endif
+! Start new residue.
+            if (res.eq.'Cl-' .or. res.eq.'Na+') then
+              ires=ires_old
+              cycle
+            else if (ibeg.eq.1) then
+c              write (iout,*) "BEG ires",ires
+              ishift=ires-1
+              if (res.ne.'GLY' .and. res.ne. 'ACE') then
+                ishift=ishift-1
+                itype(1)=ntyp1
+              endif
+              ires=ires-ishift+ishift1
+              ires_old=ires
+!              write (iout,*) "ishift",ishift," ires",ires,&
+!               " ires_old",ires_old
+              ibeg=0 
+            else if (ibeg.eq.2) then
+! Start a new chain
+              ishift=-ires_old+ires-1 !!!!!
+              ishift1=ishift1-1    !!!!!
+!              write (iout,*) "New chain started",ires,ishift,ishift1,"!"
+              ires=ires-ishift+ishift1
+              ires_old=ires
+              ibeg=0
             else
-              call sccenter(ires,iii,sccor)
+              ishift=ishift-(ires-ishift+ishift1-ires_old-1)
+              ires=ires-ishift+ishift1
+              ires_old=ires
             endif
-          endif
-C Start new residue.
-c            write (iout,'(a80)') card
-          if (ibeg.eq.1) then
-            ishift=ires-1
-            if (res.ne.'GLY' .and. res.ne. 'ACE') then
-              ishift=ishift-1
-              itype(1)=ntyp1
+            if (res.eq.'ACE' .or. res.eq.'NHE') then
+              itype(ires)=10
+            else
+              itype(ires)=rescode(ires,res,0)
             endif
-c             write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
-            ibeg=0          
-          else if (ibeg.eq.2) then
-c Start a new chain
-            ishift=-ires_old+ires-1
-c              write (iout,*) "New chain started",ires,ishift
-            ibeg=0
-          endif
-        else
-          ires=ires-ishift
-c            write (2,*) "ires",ires," ishift",ish
-        endif
-        if (atom.eq.'CA' .or. atom.eq.'CH3' .or.
-     &       res.eq.'NHE'.and.atom(:2).eq.'HN') then
-          if (res.eq.'ACE') then
-            itype(ires)=10
           else
-            itype(ires)=rescode(ires,res,0)
+            ires=ires-ishift+ishift1
           endif
-          read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
-          read(card(61:66),*) bfac(ires)
-c            if(me.eq.king.or..not.out1file)
-c     &       write (iout,'(2i3,2x,a,3f8.3)') 
-c     &       ires,itype(ires),res,(c(j,ires),j=1,3)
-          iii=1
-          do j=1,3
-            sccor(j,iii)=c(j,ires)
-          enddo
-        else if (atom.ne.'O  '.and.atom(1:1).ne.'H' .and. 
-     &             atom.ne.'N  ' .and. atom.ne.'C   ') then
+!          write (iout,*) "ires_old",ires_old," ires",ires
+          if (card(27:27).eq."A" .or. card(27:27).eq."B") then
+!            ishift1=ishift1+1
+          endif
+!          write (2,*) "ires",ires," res ",res!," ity"!,ity 
+          if (atom.eq.'CA' .or. atom.eq.'CH3' .or. 
+     &       res.eq.'NHE'.and.atom(:2).eq.'HN') then
+            read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
+!            write (iout,*) "backbone ",atom
+#ifdef DEBUG
+            write (iout,'(2i3,2x,a,3f8.3)') 
+     &      ires,itype(ires),res,(c(j,ires),j=1,3)
+#endif
             iii=iii+1
-          read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
+            do j=1,3
+              sccor(j,iii)=c(j,ires)
+            enddo
+c            write (2,*) card(23:27),ires,itype(ires),iii
+          else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and. 
+     &             atom.ne.'N' .and. atom.ne.'C' .and. 
+     &             atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and. 
+     &             atom.ne.'OXT' .and. atom(:2).ne.'3H') then
+!            write (iout,*) "sidechain ",atom
+            iii=iii+1
+            read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
+c            write (2,*) "iii",iii
+          endif
         endif
       enddo
    10 if(me.eq.king.or..not.out1file) 
      & write (iout,'(a,i5)') ' Nres: ',ires
+c      write (iout,*) "iii",iii
 C Calculate dummy residue coordinates inside the "chain" of a multichain
 C system
       nres=ires
@@ -191,6 +229,7 @@ C Calculate the CM of the last side chain.
           dc(j,ires)=sccor(j,iii)
         enddo
       else 
+c        write (iout,*) "Calling sccenter iii",iii
         call sccenter(ires,iii,sccor)
       endif
       nsup=nres
@@ -251,11 +290,15 @@ C 2/15/2013 by Adam: corrected insertion of the first dummy residue
       endif
 C Calculate internal coordinates.
       if(me.eq.king.or..not.out1file)then
-       do ires=1,nres
-        write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)') 
-     &    ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),
-     &    (c(j,nres+ires),j=1,3)
-       enddo
+      write (iout,'(/a)')
+     &  "Cartesian coordinates of the reference structure"
+      write (iout,'(a,3(3x,a5),5x,3(3x,a5))')
+     & "Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
+      do ires=1,nres
+        write (iout,'(a3,1x,i3,3f8.3,5x,3f8.3)')
+     &    restyp(itype(ires)),ires,(c(j,ires),j=1,3),
+     &    (c(j,ires+nres),j=1,3)
+      enddo
       endif
       call flush(iout)
 c      write(iout,*)"before int_from_cart nres",nres
index dc976b8..44f8459 100644 (file)
@@ -19,7 +19,6 @@ C Loop over chain permutations
       if (iz_sc.lt.2) then
         do ichain=1,nchain
           indchain=tabpermchain(ichain,iperm)
-#define DEBUG
 #ifdef DEBUG
           write (iout,*) "ichain",ichain," indchain",indchain
           write (iout,*) "chain_border",chain_border(1,ichain),
@@ -202,7 +201,6 @@ c------------------------------------------------------------------------
 #ifdef DEBUG
       write (iout,*) "nnnn",nnnn," rmsside",rmsside
 #endif
-#undef DEBUG
       rmscalc_side=rmsside
       return
       end
index cde2738..5993291 100644 (file)
@@ -1,11 +1,10 @@
       subroutine readpdb
 C Read the PDB file and convert the peptide geometry into virtual-chain 
 C geometry.
-      implicit real*8 (a-h,o-z)
+      implicit none
       include 'DIMENSIONS'
       include 'DIMENSIONS.ZSCOPT'
-      include 'DIMENSIONS.FREE'
-      include 'COMMON.FRAG'
+      include 'COMMON.CONTROL'
       include 'COMMON.LOCAL'
       include 'COMMON.VAR'
       include 'COMMON.CHAIN'
@@ -13,76 +12,88 @@ C geometry.
       include 'COMMON.IOUNITS'
       include 'COMMON.GEO'
       include 'COMMON.NAMES'
-      include 'COMMON.CONTROL'
-      integer i,j,ibeg,ishift1,ires,iii,ires_old,ishift,ity
-      logical lprn /.false./,fail
-      double precision e1(3),e2(3),e3(3)
-      double precision dcj,efree_temp
-      character*3 seq,res
-      character*5 atom
+      include 'COMMON.SBRIDGE'
+      include 'COMMON.FRAG'
+      character*3 seq,atom,res
       character*80 card
-      double precision sccor(3,20)
-      integer rescode
-      efree_temp=0.0d0
+      double precision sccor(3,50)
+      integer i,j,iii,ibeg,ishift,ishift1,ity,ires,ires_old
+      double precision dcj
+      integer rescode,kkk,lll,icha,cou,kupa,iprzes
+      logical lsecondary
+      integer iterter(maxres)
+      double precision efree_temp
       ibeg=1
       ishift1=0
-      ishift=0
-c      write (2,*) "UNRES_PDB",unres_pdb
-      ires=0
-      ires_old=0
-      iii=0
-      lsecondary=.false.
-      nhfrag=0
-      nbfrag=0
       do
         read (ipdbin,'(a80)',end=10) card
-c        write (iout,'(a)') card
+!       write (iout,'(a)') card
         if (card(:5).eq.'HELIX') then
-         nhfrag=nhfrag+1
-         lsecondary=.true.
-         read(card(22:25),*) hfrag(1,nhfrag)
-         read(card(34:37),*) hfrag(2,nhfrag)
+          nhfrag=nhfrag+1
+          lsecondary=.true.
+          read(card(22:25),*) hfrag(1,nhfrag)
+          read(card(34:37),*) hfrag(2,nhfrag)
         endif
         if (card(:5).eq.'SHEET') then
-         nbfrag=nbfrag+1
-         lsecondary=.true.
-         read(card(24:26),*) bfrag(1,nbfrag)
-         read(card(35:37),*) bfrag(2,nbfrag)
-crc----------------------------------------
-crc  to be corrected !!!
-         bfrag(3,nbfrag)=bfrag(1,nbfrag)
-         bfrag(4,nbfrag)=bfrag(2,nbfrag)
-crc----------------------------------------
+          nbfrag=nbfrag+1
+          lsecondary=.true.
+          read(card(24:26),*) bfrag(1,nbfrag)
+          read(card(35:37),*) bfrag(2,nbfrag)
+!rc----------------------------------------
+!rc  to be corrected !!!
+          bfrag(3,nbfrag)=bfrag(1,nbfrag)
+          bfrag(4,nbfrag)=bfrag(2,nbfrag)
+!rc----------------------------------------
+        endif
+        if (card(:3).eq.'END') then
+          goto 10
+        else if (card(:3).eq.'TER') then
+! End current chain
+          ires_old=ires+2
+          itype(ires_old-1)=ntyp1
+          iterter(ires_old-1)=1
+          itype(ires_old)=ntyp1
+          ishift1=ishift1+1
+          ibeg=2
+!          write (iout,*) "Chain ended",ires,ishift,ires_old
+          if (unres_pdb) then
+            do j=1,3
+              dc(j,ires)=sccor(j,iii)
+            enddo
+          else
+            call sccenter(ires,iii,sccor)
+          endif
+c          iii=0
         endif
-        if (card(:3).eq.'END' .or. card(:3).eq.'TER') goto 10
-c Read free energy
+! Read free energy
         if (index(card,"FREE ENERGY").gt.0) read(card(35:),*) efree_temp
-C Fish out the ATOM cards.
+! Fish out the ATOM cards.
         if (index(card(1:4),'ATOM').gt.0) then  
           read (card(12:16),*) atom
-c          write (iout,*) "! ",atom," !",ires
-c          if (atom.eq.'CA' .or. atom.eq.'CH3') then
+c          write (2,'(a)') card
+!          write (iout,*) "! ",atom," !",ires
+!          if (atom.eq.'CA' .or. atom.eq.'CH3') then
           read (card(23:26),*) ires
           read (card(18:20),'(a3)') res
-c          write (iout,*) "ires",ires,ires-ishift+ishift1,
-c     &      " ires_old",ires_old
-c          write (iout,*) "ishift",ishift," ishift1",ishift1
-c          write (iout,*) "IRES",ires-ishift+ishift1,ires_old
+!          write (iout,*) "ires",ires,ires-ishift+ishift1,
+!     &      " ires_old",ires_old
+!          write (iout,*) "ishift",ishift," ishift1",ishift1
+!          write (iout,*) "IRES",ires-ishift+ishift1,ires_old
           if (ires-ishift+ishift1.ne.ires_old) then
-C Calculate the CM of the preceding residue.
-c            if (ibeg.eq.0) call sccenter(ires,iii,sccor)
+! Calculate the CM of the preceding residue.
+!            if (ibeg.eq.0) call sccenter(ires,iii,sccor)
             if (ibeg.eq.0) then
-c              write (iout,*) "Calculating sidechain center iii",iii
+!              write (iout,*) "Calculating sidechain center iii",iii
               if (unres_pdb) then
                 do j=1,3
-                  dc(j,ires)=sccor(j,iii)
+                  dc(j,ires+nres)=sccor(j,iii)
                 enddo
               else
                 call sccenter(ires_old,iii,sccor)
               endif
               iii=0
             endif
-C Start new residue.
+! Start new residue.
             if (res.eq.'Cl-' .or. res.eq.'Na+') then
               ires=ires_old
               cycle
@@ -95,9 +106,17 @@ c              write (iout,*) "BEG ires",ires
               endif
               ires=ires-ishift+ishift1
               ires_old=ires
-c              write (iout,*) "ishift",ishift," ires",ires,
-c     &         " ires_old",ires_old
-              ibeg=0          
+!              write (iout,*) "ishift",ishift," ires",ires,&
+!               " ires_old",ires_old
+              ibeg=0 
+            else if (ibeg.eq.2) then
+! Start a new chain
+              ishift=-ires_old+ires-1 !!!!!
+              ishift1=ishift1-1    !!!!!
+!              write (iout,*) "New chain started",ires,ishift,ishift1,"!"
+              ires=ires-ishift+ishift1
+              ires_old=ires
+              ibeg=0
             else
               ishift=ishift-(ires-ishift+ishift1-ires_old-1)
               ires=ires-ishift+ishift1
@@ -111,15 +130,15 @@ c     &         " ires_old",ires_old
           else
             ires=ires-ishift+ishift1
           endif
-c          write (iout,*) "ires_old",ires_old," ires",ires
+!          write (iout,*) "ires_old",ires_old," ires",ires
           if (card(27:27).eq."A" .or. card(27:27).eq."B") then
-c            ishift1=ishift1+1
+!            ishift1=ishift1+1
           endif
-c          write (2,*) "ires",ires," res ",res," ity",ity
+!          write (2,*) "ires",ires," res ",res!," ity"!,ity 
           if (atom.eq.'CA' .or. atom.eq.'CH3' .or. 
      &       res.eq.'NHE'.and.atom(:2).eq.'HN') then
             read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
-c            write (iout,*) "backbone ",atom 
+!            write (iout,*) "backbone ",atom
 #ifdef DEBUG
             write (iout,'(2i3,2x,a,3f8.3)') 
      &      ires,itype(ires),res,(c(j,ires),j=1,3)
@@ -128,61 +147,82 @@ c            write (iout,*) "backbone ",atom
             do j=1,3
               sccor(j,iii)=c(j,ires)
             enddo
-            if (ishift.ne.0) then
-              ires_ca=ires+ishift-ishift1
-            else
-              ires_ca=ires
-            endif
-c            write (*,*) card(23:27),ires,itype(ires)
-          else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and.
-     &             atom.ne.'N' .and. atom.ne.'C' .and.
-     &             atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and.
+c            write (2,*) card(23:27),ires,itype(ires),iii
+          else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and. 
+     &             atom.ne.'N' .and. atom.ne.'C' .and. 
+     &             atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and. 
      &             atom.ne.'OXT' .and. atom(:2).ne.'3H') then
-c            write (iout,*) "sidechain ",atom
+!            write (iout,*) "sidechain ",atom
             iii=iii+1
             read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
+c            write (2,*) "iii",iii
           endif
         endif
       enddo
-   10 continue
-#ifdef DEBUG
-      write (iout,'(a,i5)') ' Number of residues found: ',ires
-#endif
-      if (ires.eq.0) return
-C Calculate the CM of the last side chain.
-      if (iii.gt.0)  then
-      if (unres_pdb) then
-        do j=1,3
-          dc(j,ires)=sccor(j,iii)
-        enddo
-      else
-        call sccenter(ires,iii,sccor)
-      endif
-      endif
+   10 write (iout,'(a,i5)') ' Nres: ',ires
+C Calculate dummy residue coordinates inside the "chain" of a multichain
+C system
       nres=ires
+      do i=2,nres-1
+c        write (iout,*) i,itype(i)
+
+        if (itype(i).eq.ntyp1) then
+         if (itype(i+1).eq.ntyp1) then
+C 16/01/2014 by Adasko: Adding to dummy atoms in the chain
+C first is connected prevous chain (itype(i+1).eq.ntyp1)=true
+C second dummy atom is conected to next chain itype(i+1).eq.ntyp1=false
+C           if (unres_pdb) then
+C 2/15/2013 by Adam: corrected insertion of the last dummy residue
+C            call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
+C            if (fail) then
+C              e2(1)=0.0d0
+C              e2(2)=1.0d0
+C              e2(3)=0.0d0
+C            endif !fail
+C            do j=1,3
+C             c(j,i)=c(j,i-1)-1.9d0*e2(j)
+C            enddo
+C           else   !unres_pdb
+           do j=1,3
+             dcj=(c(j,i-2)-c(j,i-3))/2.0
+             c(j,i)=c(j,i-1)+dcj
+             c(j,nres+i)=c(j,i)
+           enddo     
+C          endif   !unres_pdb
+         else     !itype(i+1).eq.ntyp1
+C          if (unres_pdb) then
+C 2/15/2013 by Adam: corrected insertion of the first dummy residue
+C            call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
+C            if (fail) then
+C              e2(1)=0.0d0
+C              e2(2)=1.0d0
+C              e2(3)=0.0d0
+C            endif
+C            do j=1,3
+C              c(j,i)=c(j,i+1)-1.9d0*e2(j)
+C            enddo
+C          else !unres_pdb
+           do j=1,3
+            dcj=(c(j,i+3)-c(j,i+2))/2.0
+            c(j,i)=c(j,i+1)-dcj
+            c(j,nres+i)=c(j,i)
+           enddo
+C          endif !unres_pdb
+         endif !itype(i+1).eq.ntyp1
+        endif  !itype.eq.ntyp1
+      enddo
+C Calculate the CM of the last side chain.
+      call sccenter(ires,iii,sccor)
       nsup=nres
       nstart_sup=1
       if (itype(nres).ne.10) then
         nres=nres+1
         itype(nres)=ntyp1
-        if (unres_pdb) then
-C 2/15/2013 by Adam: corrected insertion of the last dummy residue
-          call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
-          if (fail) then
-            e2(1)=0.0d0
-            e2(2)=1.0d0
-            e2(3)=0.0d0
-          endif
-          do j=1,3
-            c(j,nres)=c(j,nres-1)-3.8d0*e2(j)
-          enddo
-        else
         do j=1,3
-          dcj=c(j,nres-2)-c(j,nres-3)
+          dcj=(c(j,nres-2)-c(j,nres-3))/2.0
           c(j,nres)=c(j,nres-1)+dcj
           c(j,2*nres)=c(j,nres)
         enddo
-        endif
       endif
       do i=2,nres-1
         do j=1,3
@@ -196,57 +236,21 @@ C 2/15/2013 by Adam: corrected insertion of the last dummy residue
       if (itype(1).eq.ntyp1) then
         nsup=nsup-1
         nstart_sup=2
-        if (unres_pdb) then
-C 2/15/2013 by Adam: corrected insertion of the first dummy residue
-          call refsys(2,3,4,e1,e2,e3,fail)
-          if (fail) then
-            e2(1)=0.0d0
-            e2(2)=1.0d0
-            e2(3)=0.0d0
-          endif
-          do j=1,3
-            c(j,1)=c(j,2)-3.8d0*e2(j)
-          enddo
-        else
         do j=1,3
-          dcj=c(j,4)-c(j,3)
+          dcj=(c(j,4)-c(j,3))/2.0
           c(j,1)=c(j,2)-dcj
           c(j,nres+1)=c(j,1)
         enddo
-        endif
       endif
-C Copy the coordinates to reference coordinates
-c      do i=1,2*nres
-c        do j=1,3
-c          cref(j,i)=c(j,i)
-c        enddo
-c      enddo
 C Calculate internal coordinates.
-      if (lprn) then
-      write (iout,'(/a)') 
-     &  "Cartesian coordinates of the reference structure"
-      write (iout,'(a,3(3x,a5),5x,3(3x,a5))') 
-     & "Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
+      write (iout,100)
       do ires=1,nres
-        write (iout,'(a3,1x,i3,3f8.3,5x,3f8.3)') 
-     &    restyp(itype(ires)),ires,(c(j,ires),j=1,3),
-     &    (c(j,ires+nres),j=1,3)
-      enddo
-      endif
-C Calculate internal coordinates.
-       write (iout,'(a)') 
-     &   "Backbone and SC coordinates as read from the PDB"
-       do ires=1,nres
         write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)') 
      &    ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),
      &    (c(j,nres+ires),j=1,3)
-       enddo
-      call int_from_cart(.true.,.false.)
-      call sc_loc_geom(.false.)
-      do i=1,nres
-        thetaref(i)=theta(i)
-        phiref(i)=phi(i)
       enddo
+      call int_from_cart(.true.,.false.)
+      call flush(iout)
       do i=1,nres-1
         do j=1,3
           dc(j,i)=c(j,i+1)-c(j,i)
@@ -263,30 +267,24 @@ c     &   vbld_inv(i+nres)
       enddo
 c      call chainbuild
 C Copy the coordinates to reference coordinates
-      do i=1,2*nres
+      do i=1,nres
         do j=1,3
           cref(j,i)=c(j,i)
+          cref(j,i+nres)=c(j,i+nres)
         enddo
       enddo
+  100 format ('Residue    alpha-carbon coordinates    ',
+     &          '     centroid coordinates'/
+     1          '         ', 6X,'X',7X,'Y',7X,'Z',
+     &                          12X,'X',7X,'Y',7X,'Z')
+  110 format (a,'(',i3,')',6f12.5)
 
-
-      do j=1,nbfrag     
-        do i=1,4                                                       
-         bfrag(i,j)=bfrag(i,j)-ishift
-        enddo
-      enddo
-
-      do j=1,nhfrag
-        do i=1,2
-         hfrag(i,j)=hfrag(i,j)-ishift
-        enddo
-      enddo
       ishift_pdb=ishift
       return
       end
 c---------------------------------------------------------------------------
       subroutine int_from_cart(lside,lprn)
-      implicit real*8 (a-h,o-z)
+      implicit none
       include 'DIMENSIONS'
       include 'DIMENSIONS.ZSCOPT'
       include 'COMMON.LOCAL'
@@ -296,62 +294,56 @@ c---------------------------------------------------------------------------
       include 'COMMON.IOUNITS'
       include 'COMMON.GEO'
       include 'COMMON.NAMES'
-      include 'COMMON.CONTROL'
-      character*3 seq,res
-c      character*5 atom
+      character*3 seq,atom,res
       character*80 card
-      dimension sccor(3,20)
+      double precision sccor(3,50)
       integer rescode
+      double precision dist,alpha,beta,di
+      integer i,j,iti
       logical lside,lprn
-       if (lprn) then 
+      if (lprn) then 
         write (iout,'(/a)') 
      &  'Internal coordinates calculated from crystal structure.'
         if (lside) then 
           write (iout,'(8a)') '  Res  ','       dvb','     Theta',
-     & '     Gamma','    Dsc_id','       Dsc','     Alpha',
-     & '     Beta '
+     & '       Phi','    Dsc_id','       Dsc','     Alpha',
+     & '     Omega'
         else 
           write (iout,'(4a)') '  Res  ','       dvb','     Theta',
-     & '     Gamma'
+     & '       Phi'
         endif
-       endif
-      do i=1,nres-1
+      endif
+      do i=2,nres
         iti=itype(i)
-        if (dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0) then
+c        write (iout,*) i,i-1,(c(j,i),j=1,3),(c(j,i-1),j=1,3),dist(i,i-1)
+        if (itype(i-1).ne.ntyp1 .and. itype(i).ne.ntyp1 .and.
+     &    (dist(i,i-1).lt.1.0D0 .or. dist(i,i-1).gt.6.0D0)) then
           write (iout,'(a,i4)') 'Bad Cartesians for residue',i
-ctest          stop
+          stop
         endif
-        vbld(i+1)=dist(i,i+1)
-        vbld_inv(i+1)=1.0d0/vbld(i+1)
-        if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1)
+        vbld(i)=dist(i-1,i)
+        vbld_inv(i)=1.0d0/vbld(i)
+        theta(i+1)=alpha(i-1,i,i+1)
         if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
       enddo
-c      if (unres_pdb) then
-c        if (itype(1).eq.ntyp1) then
-c          theta(3)=90.0d0*deg2rad
-c          phi(4)=180.0d0*deg2rad
-c          vbld(2)=3.8d0
-c          vbld_inv(2)=1.0d0/vbld(2)
-c        endif
-c        if (itype(nres).eq.ntyp1) then
-c          theta(nres)=90.0d0*deg2rad
-c          phi(nres)=180.0d0*deg2rad
-c          vbld(nres)=3.8d0
-c          vbld_inv(nres)=1.0d0/vbld(2)
-c        endif
+c      if (itype(1).eq.ntyp1) then
+c        do j=1,3
+c          c(j,1)=c(j,2)+(c(j,3)-c(j,4))
+c        enddo
+c      endif
+c      if (itype(nres).eq.ntyp1) then
+c        do j=1,3
+c          c(j,nres)=c(j,nres-1)+(c(j,nres-2)-c(j,nres-3))
+c        enddo
 c      endif
       if (lside) then
         do i=2,nres-1
           do j=1,3
-            c(j,maxres2)=0.5D0*(2*c(j,i)+(c(j,i-1)-c(j,i))*vbld_inv(i)
-     &     +(c(j,i+1)-c(j,i))*vbld_inv(i+1))
+            c(j,maxres2)=0.5D0*(c(j,i-1)+c(j,i+1))
           enddo
           iti=itype(i)
           di=dist(i,nres+i)
-C 10/03/12 Adam: Correction for zero SC-SC bond length
-          if (itype(i).ne.10 .and. itype(i).ne.ntyp1. and. di.eq.0.0d0)
-     &     di=dsc(itype(i))
-          vbld(i+nres)=di
+           vbld(i+nres)=di
           if (itype(i).ne.10) then
             vbld_inv(i+nres)=1.0d0/di
           else
@@ -361,21 +353,41 @@ C 10/03/12 Adam: Correction for zero SC-SC bond length
             alph(i)=alpha(nres+i,i,maxres2)
             omeg(i)=beta(nres+i,i,maxres2,i+1)
           endif
-           if (lprn)
-     &     write (iout,'(a3,i4,7f10.3)') restyp(iti),i,vbld(i),
-     &     rad2deg*theta(i),rad2deg*phi(i),dsc(iti),vbld(nres+i),
-     &     rad2deg*alph(i),rad2deg*omeg(i)
+          if (iti.ne.10) then
+            alph(i)=alpha(nres+i,i,maxres2)
+            omeg(i)=beta(nres+i,i,maxres2,i+1)
+          endif
+          if (lprn)
+     &    write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
+     &    rad2deg*theta(i),rad2deg*phi(i),dsc(iti),di,
+     &    rad2deg*alph(i),rad2deg*omeg(i)
         enddo
       else if (lprn) then
         do i=2,nres
           iti=itype(i)
           write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
-     &     rad2deg*theta(i),rad2deg*phi(i)
+     &    rad2deg*theta(i),rad2deg*phi(i)
         enddo
       endif
       return
       end
-c-------------------------------------------------------------------------------
+c---------------------------------------------------------------------------
+      subroutine sccenter(ires,nscat,sccor)
+      implicit none
+      include 'DIMENSIONS'
+      include 'COMMON.CHAIN'
+      integer ires,nscat,i,j
+      double precision sccor(3,50),sccmj
+      do j=1,3
+        sccmj=0.0D0
+        do i=1,nscat
+          sccmj=sccmj+sccor(j,i) 
+        enddo
+        dc(j,ires)=sccmj/nscat
+      enddo
+      return
+      end
+c---------------------------------------------------------------------------
       subroutine sc_loc_geom(lprn)
       implicit real*8 (a-h,o-z)
       include 'DIMENSIONS'
@@ -388,6 +400,7 @@ c-------------------------------------------------------------------------------
       include 'COMMON.GEO'
       include 'COMMON.NAMES'
       include 'COMMON.CONTROL'
+      include 'COMMON.SETUP'
       double precision x_prime(3),y_prime(3),z_prime(3)
       logical lprn
       do i=1,nres-1
@@ -396,7 +409,7 @@ c-------------------------------------------------------------------------------
         enddo
       enddo
       do i=2,nres-1
-        if (itype(i).ne.10) then
+        if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
           do j=1,3
             dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i))
           enddo
@@ -416,7 +429,7 @@ c-------------------------------------------------------------------------------
         sinfac2=0.5d0/(1.0d0-costtab(i+1))
         sinfac=dsqrt(sinfac2)
         it=itype(i)
-        if (it.ne.10) then
+        if (it.ne.10 .and. itype(i).ne.ntyp1) then
 c
 C  Compute the axes of tghe local cartesian coordinates system; store in
 c   x_prime, y_prime and z_prime 
@@ -430,7 +443,10 @@ c
           x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
           y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
         enddo
+c        write (iout,*) "x_prime",(x_prime(j),j=1,3)
+c        write (iout,*) "y_prime",(y_prime(j),j=1,3)
         call vecpr(x_prime,y_prime,z_prime)
+c        write (iout,*) "z_prime",(z_prime(j),j=1,3)
 c
 C Transform the unit vector of the ith side-chain centroid, dC_norm(*,i),
 C to local coordinate system. Store in xx, yy, zz.
@@ -454,54 +470,53 @@ c
         endif
       enddo
       if (lprn) then
+        write (iout,*) "xxref,yyref,zzref"
         do i=2,nres
           iti=itype(i)
-          write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),
-     &      yyref(i),zzref(i)
+          write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),yyref(i),
+     &     zzref(i)
         enddo
       endif
       return
       end
 c---------------------------------------------------------------------------
-      subroutine sccenter(ires,nscat,sccor)
-      implicit real*8 (a-h,o-z)
-      include 'DIMENSIONS'
-      include 'COMMON.CHAIN'
-      dimension sccor(3,20)
-      do j=1,3
-        sccmj=0.0D0
-        do i=1,nscat
-          sccmj=sccmj+sccor(j,i) 
-        enddo
-        dc(j,ires)=sccmj/nscat
-      enddo
-      return
-      end
-c---------------------------------------------------------------------------
       subroutine bond_regular
-      implicit real*8 (a-h,o-z)
-      include 'DIMENSIONS'   
+      implicit none
+      include 'DIMENSIONS'
       include 'COMMON.VAR'
-      include 'COMMON.LOCAL'      
-      include 'COMMON.CALC'
+      include 'COMMON.LOCAL'
       include 'COMMON.INTERACT'
       include 'COMMON.CHAIN'
+      integer i,i1,i2
       do i=1,nres-1
        vbld(i+1)=vbl
-       vbld_inv(i+1)=1.0d0/vbld(i+1)
-       vbld(i+1+nres)=dsc(itype(i+1))
-       vbld_inv(i+1+nres)=dsc_inv(itype(i+1))
+       vbld_inv(i+1)=vblinv
+       vbld(i+1+nres)=dsc(iabs(itype(i+1)))
+       vbld_inv(i+1+nres)=dsc_inv(iabs(itype(i+1)))
 c       print *,vbld(i+1),vbld(i+1+nres)
       enddo
+c Adam 2/26/20 Alter virtual bonds for non-blocking end groups of each chain
+      do i=1,nchain
+        i1=chain_border(1,i)
+        i2=chain_border(2,i)
+        if (i1.gt.1) then
+          vbld(i1)=vbld(i1)/2
+          vbld_inv(i1)=vbld_inv(i1)*2
+        endif
+        if (i2.lt.nres) then
+          vbld(i2+1)=vbld(i2+1)/2
+          vbld_inv(i2+1)=vbld_inv(i2+1)*2
+        endif
+      enddo
       return
       end
+c---------------------------------------------------------------------------
       subroutine readpdb_template(k)
-C Read the PDB file with gaps for read_constr_homology with read2sigma
+C Read the PDB file for read_constr_homology with read2sigma
 C and convert the peptide geometry into virtual-chain geometry.
       implicit real*8 (a-h,o-z)
       include 'DIMENSIONS'
       include 'DIMENSIONS.ZSCOPT'
-      include 'DIMENSIONS.FREE'
       include 'COMMON.LOCAL'
       include 'COMMON.VAR'
       include 'COMMON.CHAIN'
@@ -510,6 +525,7 @@ C and convert the peptide geometry into virtual-chain geometry.
       include 'COMMON.GEO'
       include 'COMMON.NAMES'
       include 'COMMON.CONTROL'
+      include 'COMMON.SETUP'
       integer i,j,ibeg,ishift1,ires,iii,ires_old,ishift,ity
       logical lprn /.false./,fail
       double precision e1(3),e2(3),e3(3)
@@ -518,8 +534,10 @@ C and convert the peptide geometry into virtual-chain geometry.
       character*5 atom
       character*80 card
       double precision sccor(3,20)
-      integer rescode
-      efree_temp=0.0d0
+      integer rescode,iterter(maxres)
+      do i=1,maxres
+         iterter(i)=0
+      enddo
       ibeg=1
       ishift1=0
       ishift=0
@@ -530,10 +548,27 @@ c      write (2,*) "UNRES_PDB",unres_pdb
       lsecondary=.false.
       nhfrag=0
       nbfrag=0
-      do 
+      do
         read (ipdbin,'(a80)',end=10) card
-c        write (iout,'(a)') card
-        if (card(:3).eq.'END' .or. card(:3).eq.'TER') goto 10
+        if (card(:3).eq.'END') then
+          goto 10
+        else if (card(:3).eq.'TER') then
+C End current chain
+          ires_old=ires+2
+          itype(ires_old-1)=ntyp1 
+          iterter(ires_old-1)=1
+          itype(ires_old)=ntyp1
+          iterter(ires_old)=1
+          ibeg=2
+c          write (iout,*) "Chain ended",ires,ishift,ires_old
+          if (unres_pdb) then
+            do j=1,3
+              dc(j,ires)=sccor(j,iii)
+            enddo
+          else 
+            call sccenter(ires,iii,sccor)
+          endif
+        endif
 C Fish out the ATOM cards.
         if (index(card(1:4),'ATOM').gt.0) then  
           read (card(12:16),*) atom
@@ -547,9 +582,7 @@ c          write (iout,*) "ishift",ishift," ishift1",ishift1
 c          write (iout,*) "IRES",ires-ishift+ishift1,ires_old
           if (ires-ishift+ishift1.ne.ires_old) then
 C Calculate the CM of the preceding residue.
-c            if (ibeg.eq.0) call sccenter(ires,iii,sccor)
             if (ibeg.eq.0) then
-c              write (iout,*) "Calculating sidechain center iii",iii
               if (unres_pdb) then
                 do j=1,3
                   dc(j,ires)=sccor(j,iii)
@@ -574,6 +607,13 @@ c              write (iout,*) "BEG ires",ires
               ires_old=ires
 c              write (iout,*) "ishift",ishift," ires",ires,
 c     &         " ires_old",ires_old
+c              write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
+              ibeg=0          
+            else if (ibeg.eq.2) then
+c Start a new chain
+              ishift=-ires_old+ires-1
+              ires=ires_old+1
+c              write (iout,*) "New chain started",ires,ishift
               ibeg=0          
             else
               ishift=ishift-(ires-ishift+ishift1-ires_old-1)
@@ -589,14 +629,14 @@ c     &         " ires_old",ires_old
             ires=ires-ishift+ishift1
           endif
 c          write (iout,*) "ires_old",ires_old," ires",ires
-          if (card(27:27).eq."A" .or. card(27:27).eq."B") then
+c          if (card(27:27).eq."A" .or. card(27:27).eq."B") then
 c            ishift1=ishift1+1
-          endif
+c          endif
 c          write (2,*) "ires",ires," res ",res," ity",ity
           if (atom.eq.'CA' .or. atom.eq.'CH3' .or. 
      &       res.eq.'NHE'.and.atom(:2).eq.'HN') then
             read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
-c            write (iout,*) "backbone ",atom 
+c            write (iout,*) "backbone ",atom ,ires,res, (c(j,ires),j=1,3)
 #ifdef DEBUG
             write (iout,'(2i3,2x,a,3f8.3)') 
      &      ires,itype(ires),res,(c(j,ires),j=1,3)
@@ -621,13 +661,60 @@ c            write (iout,*) "sidechain ",atom
           endif
         endif
       enddo
-   10 continue
-#ifdef DEBUG
-      write (iout,'(a,i5)') ' Number of residues found: ',ires
-#endif
-      if (ires.eq.0) return
+   10 write (iout,'(a,i5)') ' Nres: ',ires
+C Calculate dummy residue coordinates inside the "chain" of a multichain
+C system
+      nres=ires
+      do i=2,nres-1
+c        write (iout,*) i,itype(i),itype(i+1)
+        if (itype(i).eq.ntyp1.and.iterter(i).eq.1) then
+         if (itype(i+1).eq.ntyp1.and.iterter(i+1).eq.1 ) then
+C 16/01/2014 by Adasko: Adding to dummy atoms in the chain
+C first is connected prevous chain (itype(i+1).eq.ntyp1)=true
+C second dummy atom is conected to next chain itype(i+1).eq.ntyp1=false
+           if (unres_pdb) then
+C 2/15/2013 by Adam: corrected insertion of the last dummy residue
+            call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
+            if (fail) then
+              e2(1)=0.0d0
+              e2(2)=1.0d0
+              e2(3)=0.0d0
+            endif !fail
+            do j=1,3
+             c(j,i)=c(j,i-1)-1.9d0*e2(j)
+            enddo
+           else   !unres_pdb
+           do j=1,3
+             dcj=(c(j,i-2)-c(j,i-3))/2.0
+            if (dcj.eq.0) dcj=1.23591524223
+             c(j,i)=c(j,i-1)+dcj
+             c(j,nres+i)=c(j,i)
+           enddo     
+          endif   !unres_pdb
+         else     !itype(i+1).eq.ntyp1
+          if (unres_pdb) then
+C 2/15/2013 by Adam: corrected insertion of the first dummy residue
+            call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
+            if (fail) then
+              e2(1)=0.0d0
+              e2(2)=1.0d0
+              e2(3)=0.0d0
+            endif
+            do j=1,3
+              c(j,i)=c(j,i+1)-1.9d0*e2(j)
+            enddo
+          else !unres_pdb
+           do j=1,3
+            dcj=(c(j,i+3)-c(j,i+2))/2.0
+            if (dcj.eq.0) dcj=1.23591524223
+            c(j,i)=c(j,i+1)-dcj
+            c(j,nres+i)=c(j,i)
+           enddo
+          endif !unres_pdb
+         endif !itype(i+1).eq.ntyp1
+        endif  !itype.eq.ntyp1
+      enddo
 C Calculate the CM of the last side chain.
-      if (iii.gt.0)  then
       if (unres_pdb) then
         do j=1,3
           dc(j,ires)=sccor(j,iii)
@@ -635,19 +722,31 @@ C Calculate the CM of the last side chain.
       else
         call sccenter(ires,iii,sccor)
       endif
-      endif
-      nres=ires
       nsup=nres
       nstart_sup=1
       if (itype(nres).ne.10) then
         nres=nres+1
         itype(nres)=ntyp1
+        if (unres_pdb) then
+C 2/15/2013 by Adam: corrected insertion of the last dummy residue
+          call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
+          if (fail) then
+            e2(1)=0.0d0
+            e2(2)=1.0d0
+            e2(3)=0.0d0
+          endif
+          do j=1,3
+            c(j,nres)=c(j,nres-1)-1.9d0*e2(j)
+          enddo
+        else
         do j=1,3
-          dcj=c(j,nres-2)-c(j,nres-3)
+          dcj=(c(j,nres-2)-c(j,nres-3))/2.0
+            if (dcj.eq.0) dcj=1.23591524223
           c(j,nres)=c(j,nres-1)+dcj
           c(j,2*nres)=c(j,nres)
         enddo
       endif
+      endif
       do i=2,nres-1
         do j=1,3
           c(j,i+nres)=dc(j,i)
@@ -669,18 +768,24 @@ C 2/15/2013 by Adam: corrected insertion of the first dummy residue
             e2(3)=0.0d0
           endif
           do j=1,3
-            c(j,1)=c(j,2)-3.8d0*e2(j)
+            c(j,1)=c(j,2)-1.9d0*e2(j)
           enddo
         else
         do j=1,3
-          dcj=c(j,4)-c(j,3)
+          dcj=(c(j,4)-c(j,3))/2.0
           c(j,1)=c(j,2)-dcj
           c(j,nres+1)=c(j,1)
         enddo
         endif
       endif
+C Copy the coordinates to reference coordinates
+c      do i=1,2*nres
+c        do j=1,3
+c          cref(j,i)=c(j,i)
+c        enddo
+c      enddo
 C Calculate internal coordinates.
-      if (lprn) then
+      if (out_template_coord) then
       write (iout,'(/a)') 
      &  "Cartesian coordinates of the reference structure"
       write (iout,'(a,3(3x,a5),5x,3(3x,a5))') 
@@ -692,15 +797,9 @@ C Calculate internal coordinates.
       enddo
       endif
 C Calculate internal coordinates.
-       write (iout,'(a)') 
-     &   "Backbone and SC coordinates as read from the PDB"
-       do ires=1,nres
-        write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)') 
-     &    ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),
-     &    (c(j,nres+ires),j=1,3)
-       enddo
-      call int_from_cart(.true.,.false.)
-      call sc_loc_geom(.false.)
+c      call int_from_cart1(.false.)
+      call int_from_cart(.true.,.true.)
+      call sc_loc_geom(.true.)
       do i=1,nres
         thetaref(i)=theta(i)
         phiref(i)=phi(i)
@@ -719,16 +818,19 @@ C Calculate internal coordinates.
 c        write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
 c     &   vbld_inv(i+nres)
       enddo
-c      call chainbuild
-C Copy the coordinates to reference coordinates
-      do i=1,2*nres
+      do i=1,nres
         do j=1,3
           cref(j,i)=c(j,i)
+          cref(j,i+nres)=c(j,i+nres)
+        enddo
+      enddo
+      do i=1,2*nres
+        do j=1,3
           chomo(j,i,k)=c(j,i)
         enddo
       enddo
 
-
-      ishift_pdb=ishift
       return
       end
+      
+