cluster wham readpdb & ctest ref val

diff --git a/ctest/newcorr/prota_unres_energy_check_mult.sh b/ctest/newcorr/prota_unres_energy_check_mult.sh
index 3dd5219..83b3c32 100755 (executable)
--- a/ctest/newcorr/prota_unres_energy_check_mult.sh
+++ b/ctest/newcorr/prota_unres_energy_check_mult.sh
@@ -57,7 +57,7 @@ elif [ "$1" == "1l2y_MIN_REGULAR_INT" ]; then
  fi
 
 elif [ "$1" == "1l2y_micro" ]; then
- refe="188.051"
+ refe="181.172"
  stat=`awk '{if ( $1 != "#" ) {n++;a=a+$5;a2=a2+$5^2}}END{print a/n,sqrt((a2-a^2/n)/n)}' $file_stat`
  array=(${stat// / })
  echo 'average total energy ' ${array[0]}

diff --git a/source/cluster/wham/src-HCD-5D/readpdb.F b/source/cluster/wham/src-HCD-5D/readpdb.F
index 98e538e..0167c00 100644 (file)
--- a/source/cluster/wham/src-HCD-5D/readpdb.F
+++ b/source/cluster/wham/src-HCD-5D/readpdb.F
@@ -167,45 +167,70 @@ 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 +244,12 @@ 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)') 
@@ -550,8 +556,10 @@ 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
@@ -562,10 +570,27 @@ 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 +604,7 @@ 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 +629,13 @@ 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 +651,14 @@ 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 +683,60 @@ 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 +744,31 @@ 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 +790,11 @@ 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 +840,19 @@ 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
+      
+