Adam's corrections
authorCezary Czaplewski <czarek@chem.univ.gda.pl>
Thu, 9 Apr 2020 18:57:43 +0000 (20:57 +0200)
committerCezary Czaplewski <czarek@chem.univ.gda.pl>
Thu, 9 Apr 2020 18:57:43 +0000 (20:57 +0200)
source/cluster/wham/src-HCD/readpdb.F
source/unres/src-HCD-5D/Makefile_MPICH_ifort-okeanos
source/unres/src-HCD-5D/int_from_cart.F
source/unres/src-HCD-5D/readpdb-mult.F
source/unres/src-HCD-5D/readpdb.F
source/unres/src-HCD-5D/sc_move.F
source/unres/src-HCD-5D/unres.F
source/wham/src-HCD/energy_p_new.F
source/wham/src-HCD/readpdb.F

index 98e538e..09e6e4e 100644 (file)
@@ -19,7 +19,7 @@ C geometry.
       character*3 seq,res
       character*5 atom
       character*80 card
-      double precision sccor(3,20)
+      double precision sccor(3,50)
       integer rescode
       integer iterter(maxres)
       efree_temp=0.0d0
@@ -61,6 +61,7 @@ c      write (2,*) "UNRES_PDB",unres_pdb
           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
@@ -71,7 +72,7 @@ c      write (2,*) "UNRES_PDB",unres_pdb
           else
             call sccenter(ires,iii,sccor)
           endif
-c          iii=0
+          iii=0
         endif
 ! Read free energy
         if (index(card,"FREE ENERGY").gt.0) read(card(35:),*) efree_temp
@@ -167,45 +168,70 @@ 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
@@ -219,31 +245,12 @@ 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)') 
@@ -321,7 +328,7 @@ c---------------------------------------------------------------------------
       character*3 seq,res
 c      character*5 atom
       character*80 card
-      dimension sccor(3,20)
+      dimension sccor(3,50)
       integer rescode
       logical lside,lprn
        if (lprn) then 
@@ -487,7 +494,7 @@ c---------------------------------------------------------------------------
       implicit real*8 (a-h,o-z)
       include 'DIMENSIONS'
       include 'COMMON.CHAIN'
-      dimension sccor(3,20)
+      dimension sccor(3,50)
       do j=1,3
         sccmj=0.0D0
         do i=1,nscat
@@ -549,9 +556,11 @@ C and convert the peptide geometry into virtual-chain geometry.
       character*3 seq,res
       character*5 atom
       character*80 card
-      double precision sccor(3,20)
-      integer rescode
-      efree_temp=0.0d0
+      double precision sccor(3,50)
+      integer rescode,iterter(maxres)
+      do i=1,maxres
+         iterter(i)=0
+      enddo
       ibeg=1
       ishift1=0
       ishift=0
@@ -562,10 +571,27 @@ 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
@@ -579,9 +605,7 @@ 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)
@@ -606,6 +630,13 @@ 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)
@@ -621,14 +652,14 @@ 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)
@@ -653,13 +684,60 @@ 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)
@@ -667,19 +745,31 @@ 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)
@@ -701,11 +791,11 @@ 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
@@ -751,16 +841,17 @@ 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
index ac97e59..db000f4 100644 (file)
@@ -161,7 +161,7 @@ cartder.o : cartder.F
 readpdb.o : readpdb.F
        ${FC} ${FFLAGS2} ${CPPFLAGS} readpdb.F
 
-readpdb.o : readpdb.F
+readpdb-mult.o : readpdb-mult.F
        ${FC} ${FFLAGS2} ${CPPFLAGS} readpdb-mult.F
 
 sumsld.o : sumsld.f
index 2ae703b..b36fae4 100644 (file)
@@ -227,6 +227,8 @@ c---------------------------------------------------------------------------
       integer i,j,ires,nscat
       double precision sccor(3,50)
       double precision sccmj
+      write (2,*) "sccenter",ires,nscat
+      call flush(2)
       do j=1,3
         sccmj=0.0D0
         do i=1,nscat
index 9b99e64..cc9aec9 100644 (file)
@@ -31,9 +31,10 @@ C geometry.
       lsecondary=.false.
       nhfrag=0
       nbfrag=0
+      iii=0
       do
         read (ipdbin,'(a80)',end=10) card
-!       write (iout,'(a)') card
+c        write (iout,'(a)') card
         if (card(:5).eq.'HELIX') then
           nhfrag=nhfrag+1
           lsecondary=.true.
@@ -59,9 +60,10 @@ C geometry.
           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)
@@ -69,7 +71,7 @@ C geometry.
           else
             call sccenter(ires,iii,sccor)
           endif
-c          iii=0
+          iii=0
         endif
 ! Read free energy
         if (index(card,"FREE ENERGY").gt.0) read(card(35:),*) efree_temp
@@ -77,19 +79,20 @@ c          iii=0
         if (index(card(1:4),'ATOM').gt.0) then  
           read (card(12:16),*) atom
 c          write (2,'(a)') card
-!          write (iout,*) "! ",atom," !",ires
+c          write (iout,*) "ibeg",ibeg
+c          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
+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
           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
+c              write (iout,*) "Calculating sidechain center iii",iii
               if (unres_pdb) then
                 do j=1,3
                   dc(j,ires+nres)=sccor(j,iii)
@@ -119,7 +122,7 @@ c              write (iout,*) "BEG ires",ires
 ! Start a new chain
               ishift=-ires_old+ires-1 !!!!!
               ishift1=ishift1-1    !!!!!
-!              write (iout,*) "New chain started",ires,ishift,ishift1,"!"
+c              write (iout,*) "New chain started",ires,ishift,ishift1,"!"
               ires=ires-ishift+ishift1
               ires_old=ires
               ibeg=0
@@ -136,11 +139,11 @@ c              write (iout,*) "BEG ires",ires
           else
             ires=ires-ishift+ishift1
           endif
-!          write (iout,*) "ires_old",ires_old," ires",ires
+c          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 
+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)
index 9c8462d..1ffc884 100644 (file)
@@ -1,7 +1,7 @@
       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 'COMMON.LOCAL'
       include 'COMMON.VAR'
@@ -11,33 +11,27 @@ C geometry.
       include 'COMMON.GEO'
       include 'COMMON.NAMES'
       include 'COMMON.CONTROL'
-      include 'COMMON.DISTFIT'
-      include 'COMMON.SETUP'
       include 'COMMON.FRAG'
-      integer i,j,ibeg,ishift1,ires,iii,ires_old,ishift,ity,
-     &  ishift_pdb
-      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.SETUP'
+      include 'COMMON.SBRIDGE'
+      character*3 seq,atom,res
       character*80 card
       double precision sccor(3,50)
-      integer rescode
-      efree_temp=0.0d0
+      double precision e1(3),e2(3),e3(3)
+      integer rescode,iterter(maxres),cou
+      logical fail
+      integer i,j,iii,ires,ires_old,ishift,ibeg
+      double precision dcj
+      bfac=0.0d0
+      do i=1,maxres
+         iterter(i)=0
+      enddo
       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
         if (card(:5).eq.'HELIX') then
          nhfrag=nhfrag+1
          lsecondary=.true.
@@ -55,112 +49,145 @@ crc  to be corrected !!!
          bfrag(4,nbfrag)=bfrag(2,nbfrag)
 crc----------------------------------------
         endif
-        if (card(:3).eq.'END' .or. card(:3).eq.'TER') goto 10
-c Read free energy
-        if (index(card,"FREE ENERGY").gt.0) read(card(35:),*) efree_temp
+        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
+          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
-c          write (iout,*) "! ",atom," !",ires
-c          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
-          if (ires-ishift+ishift1.ne.ires_old) then
+          read (card(14:16),'(a3)') atom
+          if (atom.eq.'CA' .or. atom.eq.'CH3') 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)
+                  dc(j,ires+nres)=sccor(j,iii)
                 enddo
               else
-                call sccenter(ires_old,iii,sccor)
+                call sccenter(ires,iii,sccor)
               endif
-              iii=0
             endif
 C 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
+c            write (iout,'(a80)') card
+            read (card(23:26),*) ires
+            read (card(18:20),'(a3)') res
+            if (ibeg.eq.1) then
               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
-c              write (iout,*) "ishift",ishift," ires",ires,
-c     &         " ires_old",ires_old
+c              write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
               ibeg=0          
-            else
-              ishift=ishift-(ires-ishift+ishift1-ires_old-1)
-              ires=ires-ishift+ishift1
-              ires_old=ires
+            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
-            if (res.eq.'ACE' .or. res.eq.'NHE') then
+            ires=ires-ishift
+c            write (2,*) "ires",ires," ishift",ishift
+            if (res.eq.'ACE') then
               itype(ires)=10
             else
               itype(ires)=rescode(ires,res,0)
             endif
-          else
-            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            ishift1=ishift1+1
-          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 
-#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(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
-            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.
-     &             atom.ne.'OXT' .and. atom(:2).ne.'3H') then
-c            write (iout,*) "sidechain ",atom
+          else if (atom.ne.'O  '.and.atom(1:1).ne.'H' .and. 
+     &             atom.ne.'N  ' .and. atom.ne.'C   ') then
             iii=iii+1
             read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
           endif
         endif
       enddo
-   10 continue
-#ifdef DEBUG
-      write (iout,'(a,i5)') ' Number of residues found: ',ires
-#endif
-      if (ires.eq.0) return
+   10 if(me.eq.king.or..not.out1file) 
+     & 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),ntyp1,iterter(i)
+        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
+            print *,i,'tu dochodze'
+            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
+            print *,i,'a tu?'
+            do j=1,3
+             c(j,i)=c(j,i-1)+1.9d0*(-e1(j)+e2(j))/sqrt(2.0d0)
+            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
+      write (iout,*) "After loop in readpbd"
 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
+      else 
         call sccenter(ires,iii,sccor)
       endif
-      endif
-      nres=ires
       nsup=nres
       nstart_sup=1
       if (itype(nres).ne.10) then
@@ -175,11 +202,12 @@ C 2/15/2013 by Adam: corrected insertion of the last dummy residue
             e2(3)=0.0d0
           endif
           do j=1,3
-            c(j,nres)=c(j,nres-1)-3.8d0*e2(j)
+            c(j,nres)=c(j,nres-1)+1.9d0*(-e1(j)+e2(j))/sqrt(2.0d0)
           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
@@ -206,46 +234,27 @@ 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*(e1(j)-e2(j))/dsqrt(2.0d0)
           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)"
-      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.
       if(me.eq.king.or..not.out1file)then
-       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
       endif
+      call flush(iout)
+c      write(iout,*)"before int_from_cart nres",nres
       call int_from_cart(.true.,.false.)
-      call sc_loc_geom(.false.)
       do i=1,nres
         thetaref(i)=theta(i)
         phiref(i)=phi(i)
@@ -255,6 +264,8 @@ C Calculate internal coordinates.
           dc(j,i)=c(j,i+1)-c(j,i)
           dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
         enddo
+c        write (iout,*) i,(dc(j,i),j=1,3),(dc_norm(j,i),j=1,3),
+c     &   vbld_inv(i+1)
       enddo
       do i=2,nres-1
         do j=1,3
@@ -264,15 +275,22 @@ 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
+      call sc_loc_geom(.false.)
+      call int_from_cart1(.false.)
 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 (//'              alpha-carbon coordinates       ',
+     &          '     centroid coordinates'/
+     1          '       ', 6X,'X',11X,'Y',11X,'Z',
+     &                          10X,'X',11X,'Y',11X,'Z')
+  110 format (a,'(',i3,')',6f12.5)
+cc enddiag
       do j=1,nbfrag     
         do i=1,4                                                       
          bfrag(i,j)=bfrag(i,j)-ishift
@@ -284,14 +302,13 @@ C Copy the coordinates to reference coordinates
          hfrag(i,j)=hfrag(i,j)-ishift
         enddo
       enddo
-      ishift_pdb=ishift
       return
       end
-c-----------------------------------------------------------------------
+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)
+      implicit none
       include 'DIMENSIONS'
       include 'COMMON.LOCAL'
       include 'COMMON.VAR'
@@ -301,20 +318,21 @@ C and convert the peptide geometry into virtual-chain geometry.
       include 'COMMON.GEO'
       include 'COMMON.NAMES'
       include 'COMMON.CONTROL'
-      include 'COMMON.DISTFIT'
+      include 'COMMON.FRAG'
       include 'COMMON.SETUP'
-      include 'COMMON.MD'
-      integer i,j,ibeg,ishift1,ires,iii,ires_old,ishift,ity,
-     &  ishift_pdb
+      integer i,j,k,ibeg,ishift1,ires,iii,ires_old,ishift,ity,
+     &  ishift_pdb,ires_ca
       logical lprn /.false./,fail
       double precision e1(3),e2(3),e3(3)
       double precision dcj,efree_temp
       character*3 seq,res
       character*5 atom
       character*80 card
-      double precision sccor(3,50)
-      integer rescode
-      efree_temp=0.0d0
+      double precision sccor(3,20)
+      integer rescode,iterter(maxres)
+      do i=1,maxres
+         iterter(i)=0
+      enddo
       ibeg=1
       ishift1=0
       ishift=0
@@ -325,10 +343,27 @@ 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
@@ -342,9 +377,7 @@ 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)
@@ -369,6 +402,13 @@ 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)
@@ -384,14 +424,14 @@ 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)
@@ -416,13 +456,61 @@ 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 if(me.eq.king.or..not.out1file) 
+     & 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)
@@ -430,19 +518,31 @@ 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)
@@ -464,18 +564,24 @@ 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))') 
@@ -487,16 +593,7 @@ C Calculate internal coordinates.
       enddo
       endif
 C Calculate internal coordinates.
-      if(me.eq.king.or..not.out1file)then
-       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
-      endif
-      call int_from_cart(.true.,.false.)
+      call int_from_cart(.true.,.true.)
       call sc_loc_geom(.false.)
       do i=1,nres
         thetaref(i)=theta(i)
@@ -516,16 +613,18 @@ 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
+      
index 201e20f..7911b30 100644 (file)
@@ -369,7 +369,7 @@ c      parameter (liv=60,lv=(77+maxvar*(maxvar+17)/2))
       external funcgrad_restr1
       external optsave
 #else
-      external func,gradient,fdum
+      external fdum
       external func_restr1,grad_restr1
       logical not_done,change,reduce 
       dimension iv(liv)                                               
index 08caade..be40e75 100644 (file)
@@ -339,6 +339,7 @@ c          print *,'Calling MINIMIZE.'
           potE=etot
           call cartoutx(0.0d0)
         endif
+        if (outpdb) call pdbout(etot,titel(:50),ipdb)
         if (refstr) call rms_nac_nnc(rms,frac,frac_nn,co,.true.)
 #ifdef LBFGS
           write (iout,'(a,a9)') 'LBFGS return code:',status
index 835045b..bd69774 100644 (file)
@@ -20,6 +20,7 @@ cMS$ATTRIBUTES C ::  proc_proc
       include 'COMMON.SHIELD'
       include 'COMMON.CONTROL'
       include 'COMMON.TORCNSTR'
+      include 'COMMON.SAXS'
       double precision fact(6)
 c      write(iout, '(a,i2)')'Calling etotal ipot=',ipot
 c      call flush(iout)
@@ -179,12 +180,16 @@ c      write(iout,*) "TEST_ENE1 constr_homology=",constr_homology
 c      write(iout,*) "TEST_ENE1 ehomology_constr=",ehomology_constr
 #ifdef DFA
 C     BARTEK for dfa test!
+      edfadis=0.0d0
       if (wdfa_dist.gt.0) call edfad(edfadis)
 c      write(iout,*)'edfad is finished!', wdfa_dist,edfadis
+      edfator=0.0d0
       if (wdfa_tor.gt.0) call edfat(edfator)
 c      write(iout,*)'edfat is finished!', wdfa_tor,edfator
+      edfanei=0.0d0
       if (wdfa_nei.gt.0) call edfan(edfanei)
 c      write(iout,*)'edfan is finished!', wdfa_nei,edfanei
+      edfabet=0.0d0
       if (wdfa_beta.gt.0) call edfab(edfabet)
 c      write(iout,*)'edfab is finished!', wdfa_beta,edfabet
 #endif
index 5993291..855d754 100644 (file)
@@ -23,6 +23,7 @@ C geometry.
       logical lsecondary
       integer iterter(maxres)
       double precision efree_temp
+      iii=0
       ibeg=1
       ishift1=0
       do
@@ -53,6 +54,7 @@ C geometry.
           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
@@ -63,7 +65,7 @@ C geometry.
           else
             call sccenter(ires,iii,sccor)
           endif
-c          iii=0
+          iii=0
         endif
 ! Read free energy
         if (index(card,"FREE ENERGY").gt.0) read(card(35:),*) efree_temp