Adam's changes

diff --git a/source/cluster/wham/src-HCD/readpdb.F b/source/cluster/wham/src-HCD/readpdb.F
index 09e6e4e..a7bb52b 100644 (file)
--- a/source/cluster/wham/src-HCD/readpdb.F
+++ b/source/cluster/wham/src-HCD/readpdb.F
@@ -13,7 +13,7 @@ C geometry.
       include 'COMMON.NAMES'
       include 'COMMON.CONTROL'
       integer i,j,ibeg,ishift1,ires,iii,ires_old,ishift,ity
-      logical lprn /.false./,fail
+      logical lprn /.false./,fail,sccalc
       double precision e1(3),e2(3),e3(3)
       double precision dcj,efree_temp
       character*3 seq,res
@@ -30,6 +30,7 @@ c      write (2,*) "UNRES_PDB",unres_pdb
       ires=0
       ires_old=0
       iii=0
+      sccalc=.false.
       lsecondary=.false.
       nhfrag=0
       nbfrag=0
@@ -73,11 +74,13 @@ c      write (2,*) "UNRES_PDB",unres_pdb
             call sccenter(ires,iii,sccor)
           endif
           iii=0
+          sccalc=.true.
         endif
 ! 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  
+          sccalc=.false.
           read (card(12:16),*) atom
 c          write (2,'(a)') card
 !          write (iout,*) "! ",atom," !",ires
@@ -101,6 +104,7 @@ c          write (2,'(a)') card
                 call sccenter(ires_old,iii,sccor)
               endif
               iii=0
+              sccalc=.true.
             endif
 ! Start new residue.
             if (res.eq.'Cl-' .or. res.eq.'Na+') then
@@ -221,7 +225,7 @@ C          endif !unres_pdb
         endif  !itype.eq.ntyp1
       enddo
 C Calculate the CM of the last side chain.
-      call sccenter(ires,iii,sccor)
+      if (.not.sccalc) call sccenter(ires,iii,sccor)
       nsup=nres
       nstart_sup=1
       if (itype(nres).ne.10) then

diff --git a/source/unres/src-HCD-5D/COMMON.INTERACT b/source/unres/src-HCD-5D/COMMON.INTERACT
index 6db43d0..8e4e063 100644 (file)
--- a/source/unres/src-HCD-5D/COMMON.INTERACT
+++ b/source/unres/src-HCD-5D/COMMON.INTERACT
@@ -22,10 +22,10 @@
      & iatsc_s,iatsc_e,iatel_s,iatel_e,iatel_s_vdw,iatel_e_vdw,
      & iatscp_s,iatscp_e,ispp,iscp
 C 3/26/20 Interaction lists
-      integer newcontlisti(200*maxres),newcontlistj(200*maxres),
-     & newcontlistppi(200*maxres),newcontlistppj(200*maxres),
-     & newcontlistpp_vdwi(200*maxres),newcontlistpp_vdwj(200*maxres),
-     & newcontlistscpi(200*maxres),newcontlistscpj(200*maxres),
+      integer newcontlisti(2000*maxres),newcontlistj(2000*maxres),
+     & newcontlistppi(2000*maxres),newcontlistppj(2000*maxres),
+     & newcontlistpp_vdwi(2000*maxres),newcontlistpp_vdwj(2000*maxres),
+     & newcontlistscpi(2000*maxres),newcontlistscpj(2000*maxres),
      & g_listscsc_start,g_listscsc_end,g_listpp_start,g_listpp_end,
      & g_listpp_vdw_start,g_listpp_vdw_end,g_listscp_start,g_listscp_end
       common /interact_list/newcontlisti,newcontlistj,g_listscsc_start,

diff --git a/source/unres/src-HCD-5D/DIMENSIONS b/source/unres/src-HCD-5D/DIMENSIONS
index 113d3d2..75287f5 100644 (file)
--- a/source/unres/src-HCD-5D/DIMENSIONS
+++ b/source/unres/src-HCD-5D/DIMENSIONS
@@ -16,7 +16,7 @@ C Max. number of coarse-grain processors
       parameter (max_cg_procs=maxprocs)
 C Max. number of AA residues
       integer maxres
-      parameter (maxres=3300)
+      parameter (maxres=5000)
 C Max. number of AA residues per chain
       integer maxres_chain
       parameter (maxres_chain=1200)
@@ -40,7 +40,8 @@ C Max. number of groups of interactions that a given SC is involved in
 C Max. number of derivatives of virtual-bond and side-chain vectors in theta
 C or phi.
       integer maxdim
-      parameter (maxdim=(maxres_chain-1)*(maxres_chain-2)/2)
+c      parameter (maxdim=(maxres_chain-1)*(maxres_chain-2)/2)
+      parameter (maxdim=(maxres-1)*(maxres-2)/2)
 C Max. number of SC contacts
       integer maxcont
       parameter (maxcont=12*maxres)

diff --git a/source/unres/src-HCD-5D/MD_A-MTS.F b/source/unres/src-HCD-5D/MD_A-MTS.F
index 4498b4a..d82cf17 100644 (file)
--- a/source/unres/src-HCD-5D/MD_A-MTS.F
+++ b/source/unres/src-HCD-5D/MD_A-MTS.F
@@ -1965,12 +1965,12 @@ c 8/22/17 AL Loop to produce a low-energy random conformation
                   cycle
                 endif
               endif
-#ifdef SEARCHSC
               if (me.eq.king.or..not.out1file) then
               write (iout,*) "Energies after removing overlaps"
               call etotal(energia(0))
               call enerprint(energia(0))
               endif
+#ifdef SEARCHSC
 ! Search for better SC rotamers if requested
               if (searchsc) then
                 call sc_move(2,nres-1,10,1d10,nft_sc,etot)
@@ -1987,6 +1987,21 @@ c 8/22/17 AL Loop to produce a low-energy random conformation
               iranconf=1
               goto 122
             endif
+          else
+! Remove SC overlaps if requested
+              if (overlapsc) then
+                write (iout,*) 'Calling OVERLAP_SC'
+                call overlap_sc(fail)
+                if (fail) then 
+                  write (iout,*) 
+     &            "Failed to remove overlap"
+                endif
+              endif
+              if (me.eq.king.or..not.out1file) then
+              write (iout,*) "Energies after removing overlaps"
+              call etotal(energia(0))
+              call enerprint(energia(0))
+              endif
           endif
 C 8/22/17 AL Minimize initial structure
           if (dccart) then

diff --git a/source/unres/src-HCD-5D/Makefile_MPICH_ifort-okeanos b/source/unres/src-HCD-5D/Makefile_MPICH_ifort-okeanos
index db000f4..b851430 100644 (file)
--- a/source/unres/src-HCD-5D/Makefile_MPICH_ifort-okeanos
+++ b/source/unres/src-HCD-5D/Makefile_MPICH_ifort-okeanos
@@ -4,11 +4,11 @@
 
 FC = ftn
 
-#OPT =  -O3 -ip -mcmodel=medium -shared-intel -dynamic
-OPT =  -g -CA -CB -mcmodel=medium -shared-intel -dynamic
+OPT =  -O3 -ip -mcmodel=medium -shared-intel -dynamic
+#OPT =  -g -CA -CB -mcmodel=medium -shared-intel -dynamic
 OPT2 = -g -O0 -mcmodel=medium -shared-intel -dynamic
-#OPTE = -c  -O3 -ipo  -mcmodel=medium -shared-intel -dynamic
-OPTE = ${OPT} -c
+OPTE = -c  -O3 -ipo  -mcmodel=medium -shared-intel -dynamic
+#OPTE = ${OPT} -c
 
 FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include 
 #FFLAGS1 = -c  -g -CA -CB -I$(INSTALL_DIR)/include 
@@ -94,6 +94,24 @@ E0LL2Y_DFA: ${object} dfa.o xdrf/libxdrf.a
        ${FC} ${FFLAGS} cinfo.f
        ${FC} ${OPT} ${object} dfa.o cinfo.o ${LIBS}  -o ${BIN}
 
+E0LL2Y5D: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+       -DSPLITELE -DLANG0 -DFIVEDIAG
+E0LL2Y5D: BIN = ~/bin/unres_ifort_MPICH-okeanos_E0LL2Y-HCD5.exe
+E0LL2Y5D: ${object} xdrf/libxdrf.a
+       gcc -o compinfo compinfo.c
+       ./compinfo | true
+       ${FC} ${FFLAGS} cinfo.f
+       ${FC} ${OPT} ${object} cinfo.o ${LIBS}  -o ${BIN}
+
+E0LL2Y5D_DFA: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
+       -DSPLITELE -DLANG0 -DFIVEDIAG -DDFA
+E0LL2Y5D_DFA: BIN = ~/bin/unres_ifort_MPICH-okeanos_E0LL2Y-HCD5-DFA.exe
+E0LL2Y5D_DFA: ${object} dfa.o xdrf/libxdrf.a
+       gcc -o compinfo compinfo.c
+       ./compinfo | true
+       ${FC} ${FFLAGS} cinfo.f
+       ${FC} ${OPT} ${object} dfa.o cinfo.o ${LIBS}  -o ${BIN}
+
 NEWCORR: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
        -DSPLITELE -DLANG0 -DNEWCORR -DCORRCD #-DFOURBODY #-DMYGAUSS #-DTIMING
 NEWCORR: BIN = ~/bin/unres_ifort_MPICH-okeanos_SC-HCD.exe

diff --git a/source/unres/src-HCD-5D/cartprint.f b/source/unres/src-HCD-5D/cartprint.f
index 9f7eacb..339a89d 100644 (file)
--- a/source/unres/src-HCD-5D/cartprint.f
+++ b/source/unres/src-HCD-5D/cartprint.f
@@ -13,8 +13,8 @@
       enddo
   100 format (//'              alpha-carbon coordinates       ',
      &          '     centroid coordinates'/
-     1          '       ', 6X,'X',11X,'Y',11X,'Z',
+     1          '       ', 7X,'X',11X,'Y',11X,'Z',
      &                          10X,'X',11X,'Y',11X,'Z')
-  110 format (a,'(',i3,')',6f12.5)
+  110 format (a,'(',i4,')',6f12.5)
       return
       end  

diff --git a/source/unres/src-HCD-5D/contact.f b/source/unres/src-HCD-5D/contact.f
index 695446f..f986380 100644 (file)
--- a/source/unres/src-HCD-5D/contact.f
+++ b/source/unres/src-HCD-5D/contact.f
@@ -38,7 +38,7 @@ c         print *,'rcomp=',rcomp,' dist=',dist(nres+i,nres+j)
           i2=icont(2,i)
           it1=itype(i1)
           it2=itype(i2)
-          write (iout,'(i3,2x,a,i4,2x,a,i4)') 
+          write (iout,'(i5,2x,a,i5,2x,a,i4)') 
      &     i,restyp(it1),i1,restyp(it2),i2 
         enddo
       endif
@@ -137,7 +137,7 @@ c     print *,'nnt=',nnt,' nct=',nct
           i2=icont(2,i)
           it1=itype(i1)
           it2=itype(i2)
-          write (iout,'(i3,2x,a,i4,2x,a,i4)') 
+          write (iout,'(i5,2x,a,i5,2x,a,i4)') 
      &     i,restyp(it1),i1,restyp(it2),i2 
         enddo
       endif
@@ -184,8 +184,8 @@ c      enddo
         ii1=iharp(3,i)
         jj1=iharp(4,i)
         write (iout,*)
-        write (iout,'(20(a,i3,1x))') (restyp(itype(k)),k,k=i1,ii1)
-        write (iout,'(20(a,i3,1x))') (restyp(itype(k)),k,k=j1,jj1,-1)
+        write (iout,'(20(a,i5,1x))') (restyp(itype(k)),k,k=i1,ii1)
+        write (iout,'(20(a,i5,1x))') (restyp(itype(k)),k,k=j1,jj1,-1)
 c        do k=jj1,j1,-1
 c         write (iout,'(a,i3,$)') restyp(itype(k)),k
 c        enddo

diff --git a/source/unres/src-HCD-5D/energy_p_new_barrier.F b/source/unres/src-HCD-5D/energy_p_new_barrier.F
index ddc2a4d..07cdebb 100644 (file)
--- a/source/unres/src-HCD-5D/energy_p_new_barrier.F
+++ b/source/unres/src-HCD-5D/energy_p_new_barrier.F
@@ -2053,6 +2053,9 @@ C derivatives.
               sigsq=1.0D0/sigsq
               sig=sig0ij*dsqrt(sigsq)
               rij_shift=1.0D0/rij-sig+sig0ij
+c              if (energy_dec)
+c     &        write (iout,*) "rij",1.0d0/rij," rij_shift",rij_shift,
+c     &       " sig",sig," sig0ij",sig0ij
 c for diagnostics; uncomment
 c            rij_shift=1.2*sig0ij
 C I hate to put IF's in the loops, but here don't have another choice!!!!
@@ -2061,7 +2064,7 @@ C I hate to put IF's in the loops, but here don't have another choice!!!!
 cd              write (iout,'(2(a3,i3,2x),17(0pf7.3))')
 cd     &        restyp(itypi),i,restyp(itypj),j,
 cd     &        rij_shift,1.0D0/rij,sig,sig0ij,sigsq,1-dsqrt(sigsq) 
-                return
+c                return
               endif
               sigder=-sig*sigsq
 c---------------------------------------------------------------
@@ -2093,7 +2096,7 @@ c     &        " eps3rt",eps3rt," eps1",eps1," e1",e1," e2",e2
      &           evdwij
               endif
 
-              if (energy_dec) write (iout,'(a,2i5,3f10.5)') 
+              if (energy_dec) write (iout,'(a,2i5,2f10.5,e15.5)') 
      &                    'r sss evdw',i,j,1.0d0/rij,sss,evdwij
 
 C Calculate gradient components.

diff --git a/source/unres/src-HCD-5D/gen_rand_conf.F b/source/unres/src-HCD-5D/gen_rand_conf.F
index 557f435..b5e5595 100644 (file)
--- a/source/unres/src-HCD-5D/gen_rand_conf.F
+++ b/source/unres/src-HCD-5D/gen_rand_conf.F
@@ -780,7 +780,7 @@ c     overlapping residues left, or false otherwise (success)
       call overlap_sc_list(ioverlap,ioverlap_last)
       if (ioverlap_last.gt.0) then
         write (iout,*) '#OVERLAPing residues ',ioverlap_last
-        write (iout,'(20i4)') (ioverlap(k),k=1,ioverlap_last)
+        write (iout,'(18i5)') (ioverlap(k),k=1,ioverlap_last)
         had_overlaps=.true.
       endif
 
@@ -845,13 +845,15 @@ c     overlapping residues left, or false otherwise (success)
       integer ioverlap(maxres),ioverlap_last
       data redfac /0.5D0/
 
-c      write (iout,*) "overlap_sc_list"
+      write (iout,*) "overlap_sc_list"
+c      write(iout,*) "iatsc_s",iatsc_s," iatsc_e",iatsc_e
+      write(iout,*) "nnt",nnt," nct",nct
       ioverlap_last=0
 C Check for SC-SC overlaps and mark residues
 c      print *,'>>overlap_sc nnt=',nnt,' nct=',nct
       ind=0
-c      write(iout,*) "iatsc_s",iatsc_s," iatsc_e",iatsc_e
-      do i=iatsc_s,iatsc_e
+c      do i=iatsc_s,iatsc_e
+      do i=nnt,nct
         itypi=iabs(itype(i))
         itypi1=iabs(itype(i+1))
         if (itypi.eq.ntyp1) cycle
@@ -863,12 +865,13 @@ c      write(iout,*) "iatsc_s",iatsc_s," iatsc_e",iatsc_e
         dzi=dc_norm(3,nres+i)
         dsci_inv=dsc_inv(itypi)
 c
-       do iint=1,nint_gr(i)
-         do j=istart(i,iint),iend(i,iint)
+c        do iint=1,nint_gr(i)
+c          do j=istart(i,iint),iend(i,iint)
+          do j=i+1,nct
             ind=ind+1
             itypj=iabs(itype(j))
             if (itypj.eq.ntyp1) cycle
-c            write (iout,*) "i,j",i,j," itypi,itypj",itypi,itypj
+c           write (iout,*) "i,j",i,j," itypi,itypj",itypi,itypj
             dscj_inv=dsc_inv(itypj)
             sig0ij=sigma(itypi,itypj)
             chi1=chi(itypi,itypj)
@@ -880,13 +883,13 @@ c            write (iout,*) "i,j",i,j," itypi,itypj",itypi,itypj
             alf1=alp(itypi)   
             alf2=alp(itypj)   
             alf12=0.5D0*(alf1+alf2)
-          if (j.gt.i+1) then
-           rcomp=sigmaii(itypi,itypj)
-          else 
-           rcomp=sigma(itypi,itypj)
-          endif
-c          write (iout,'(2(a3,2i3),a3,2f10.5)'),
-c     &        ' i=',i,iti,' j=',j,itj,' d=',dist(nres+i,nres+j)
+            if (j.gt.i+1) then
+              rcomp=sigmaii(itypi,itypj)
+            else 
+              rcomp=sigma(itypi,itypj)
+            endif
+c            write (iout,'(2(a3,2i5),a3,2f10.5)'),
+c     &        ' i=',i,itypi,' j=',j,itypj,' d=',dist(nres+i,nres+j)
 c     &        ,rcomp
             xj=c(1,nres+j)-xi
             yj=c(2,nres+j)-yi
@@ -905,28 +908,28 @@ c            write (iout,*) "sigsq",sigsq
             sigsq=1.0D0/sigsq
             sig=sig0ij*dsqrt(sigsq)
             rij_shift=1.0D0/rij-sig+sig0ij
-c            write (iout,*) "rij_shift",rij_shift
-c          if ( 1.0/rij .lt. redfac*rcomp .or. 
-c     &       rij_shift.le.0.0D0 ) then
-c          write (iout,'(a,i3,a,i3,a,f10.5,a,3f10.5)')
-c     &     'overlap SC-SC: i=',i,' j=',j,
-c     &     ' dist=',dist(nres+i,nres+j),' rcomp=',
-c     &     rcomp,1.0/rij,rij_shift
-            if ( rij_shift.le.0.0D0 ) then
-c                    write (iout,*) "overlap",i,j
-          ioverlap_last=ioverlap_last+1
-          ioverlap(ioverlap_last)=i         
-          do k=1,ioverlap_last-1
-           if (ioverlap(k).eq.i) ioverlap_last=ioverlap_last-1
+c            write (iout,*) "rij",1.0d0/rij," rij_shift",rij_shift,
+c     &       " sig",sig," sig0ij",sig0ij
+c            if ( rij_shift.le.0.0D0 ) then
+            if ( rij_shift/sig0ij.le.0.1D0 ) then
+c              write (iout,*) "overlap",i,j
+              write (iout,'(a,i5,a,i5,a,f10.5,a,3f10.5)')
+     &         'overlap SC-SC: i=',i,' j=',j,
+     &         ' dist=',dist(nres+i,nres+j),' rcomp=',
+     &         rcomp,1.0/rij,rij_shift
+              ioverlap_last=ioverlap_last+1
+              ioverlap(ioverlap_last)=i         
+              do k=1,ioverlap_last-1
+                if (ioverlap(k).eq.i) ioverlap_last=ioverlap_last-1
+              enddo
+              ioverlap_last=ioverlap_last+1
+              ioverlap(ioverlap_last)=j         
+              do k=1,ioverlap_last-1
+                if (ioverlap(k).eq.j) ioverlap_last=ioverlap_last-1
+              enddo 
+            endif
           enddo
-          ioverlap_last=ioverlap_last+1
-          ioverlap(ioverlap_last)=j         
-          do k=1,ioverlap_last-1
-           if (ioverlap(k).eq.j) ioverlap_last=ioverlap_last-1
-          enddo 
-         endif
-        enddo
-       enddo
+c        enddo
       enddo
       return
       end

diff --git a/source/unres/src-HCD-5D/geomout.F b/source/unres/src-HCD-5D/geomout.F
index dd45a7d..d1a3a87 100644 (file)
--- a/source/unres/src-HCD-5D/geomout.F
+++ b/source/unres/src-HCD-5D/geomout.F
@@ -224,11 +224,11 @@ c------------------------------------------------------------------------
       include 'COMMON.TORSION'
       integer i,iti
       write (iout,'(/a)') 'Geometry of the virtual chain.'
-      write (iout,'(7a)') '  Res  ','         d','     Theta',
+      write (iout,'(7a)') '  Res   ','         d','     Theta',
      & '       Phi','       Dsc','     Alpha','      Omega'
       do i=1,nres
        iti=itype(i)
-        write (iout,'(a3,i4,6f10.3)') restyp(iti),i,vbld(i),
+        write (iout,'(a3,i5,6f10.3)') restyp(iti),i,vbld(i),
      &     rad2deg*theta(i),rad2deg*phi(i),vbld(nres+i),rad2deg*alph(i),
      &     rad2deg*omeg(i)
       enddo

diff --git a/source/unres/src-HCD-5D/int_from_cart.F b/source/unres/src-HCD-5D/int_from_cart.F
index b36fae4..ded15f9 100644 (file)
--- a/source/unres/src-HCD-5D/int_from_cart.F
+++ b/source/unres/src-HCD-5D/int_from_cart.F
@@ -227,8 +227,8 @@ c---------------------------------------------------------------------------
       integer i,j,ires,nscat
       double precision sccor(3,50)
       double precision sccmj
-      write (2,*) "sccenter",ires,nscat
-      call flush(2)
+c      write (2,*) "sccenter",ires,nscat
+c      call flush(2)
       do j=1,3
         sccmj=0.0D0
         do i=1,nscat

diff --git a/source/unres/src-HCD-5D/make_xx_list.F b/source/unres/src-HCD-5D/make_xx_list.F
index a83740f..a69ee13 100644 (file)
--- a/source/unres/src-HCD-5D/make_xx_list.F
+++ b/source/unres/src-HCD-5D/make_xx_list.F
@@ -12,7 +12,7 @@
       double precision xi,yi,zi,xj,yj,zj,xj_safe,yj_safe,zj_safe,
      &  xj_temp,yj_temp,zj_temp
       double precision dist_init, dist_temp,r_buff_list
-      integer contlisti(200*maxres),contlistj(200*maxres)
+      integer contlisti(2000*maxres),contlistj(2000*maxres)
 !      integer :: newcontlisti(200*nres),newcontlistj(200*nres) 
       integer i,j,itypi,itypj,subchap,xshift,yshift,zshift,iint,
      &  ilist_sc,g_ilist_sc
@@ -164,12 +164,12 @@ c        write(iout,*) "before bcast",g_ilist_sc
       double precision xi,yi,zi,xj,yj,zj,xj_safe,yj_safe,zj_safe,
      &  xj_temp,yj_temp,zj_temp
       double precision dist_init, dist_temp,r_buff_list
-      integer contlistscpi(200*maxres),contlistscpj(200*maxres)
+      integer contlistscpi(2000*maxres),contlistscpj(2000*maxres)
 !      integer :: newcontlistscpi(200*nres),newcontlistscpj(200*nres)
       integer i,j,itypi,itypj,subchap,xshift,yshift,zshift,iint,
      &  ilist_scp,g_ilist_scp
       integer displ(0:max_fg_procs),i_ilist_scp(0:max_fg_procs),ierr
-      integer contlistscpi_f(200*maxres),contlistscpj_f(200*maxres)
+      integer contlistscpi_f(2000*maxres),contlistscpj_f(2000*maxres)
       integer ilist_scp_first,ifirstrun,g_ilist_sc
 !            print *,"START make_SC"
 #ifdef DEBUG
@@ -349,7 +349,7 @@ c        write(iout,*) "before bcast",g_ilist_sc
      &  xmedi,ymedi,zmedi
       double precision dx_normi,dy_normi,dz_normi,dxj,dyj,dzj,
      &  dx_normj,dy_normj,dz_normj
-      integer contlistpp_vdwi(200*maxres),contlistpp_vdwj(200*maxres)
+      integer contlistpp_vdwi(2000*maxres),contlistpp_vdwj(2000*maxres)
 !      integer :: newcontlistppi(200*nres),newcontlistppj(200*nres)
       integer i,j,itypi,itypj,subchap,xshift,yshift,zshift,iint,
      &  ilist_pp_vdw,g_ilist_pp_vdw
@@ -509,7 +509,7 @@ c        write(iout,*) "before bcast",g_ilist_sc
      &  xmedi,ymedi,zmedi
       double precision dx_normi,dy_normi,dz_normi,dxj,dyj,dzj,
      &  dx_normj,dy_normj,dz_normj
-      integer contlistppi(200*maxres),contlistppj(200*maxres)
+      integer contlistppi(2000*maxres),contlistppj(2000*maxres)
 !      integer :: newcontlistppi(200*nres),newcontlistppj(200*nres)
       integer i,j,itypi,itypj,subchap,xshift,yshift,zshift,iint,
      &  ilist_pp,g_ilist_pp

diff --git a/source/unres/src-HCD-5D/readpdb-mult.F b/source/unres/src-HCD-5D/readpdb-mult.F
index cc9aec9..40bf9ac 100644 (file)
--- a/source/unres/src-HCD-5D/readpdb-mult.F
+++ b/source/unres/src-HCD-5D/readpdb-mult.F
@@ -19,7 +19,7 @@ C geometry.
       double precision sccor(3,50)
       double precision e1(3),e2(3),e3(3)
       integer rescode,iterter(maxres),cou
-      logical fail
+      logical fail,sccalc
       integer i,j,iii,ires,ires_old,ishift,ishift1,ibeg
       double precision dcj,efree_temp
       bfac=0.0d0
@@ -32,6 +32,7 @@ C geometry.
       nhfrag=0
       nbfrag=0
       iii=0
+      sccalc=.false.
       do
         read (ipdbin,'(a80)',end=10) card
 c        write (iout,'(a)') card
@@ -72,11 +73,13 @@ c        write (iout,'(a)') card
             call sccenter(ires,iii,sccor)
           endif
           iii=0
+          sccalc=.true.
         endif
 ! 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  
+          sccalc=.false.
           read (card(12:16),*) atom
 c          write (2,'(a)') card
 c          write (iout,*) "ibeg",ibeg
@@ -101,6 +104,7 @@ c              write (iout,*) "Calculating sidechain center iii",iii
                 call sccenter(ires_old,iii,sccor)
               endif
               iii=0
+              sccalc=.true.
             endif
 ! Start new residue.
             if (res.eq.'Cl-' .or. res.eq.'Na+') then
@@ -200,6 +204,7 @@ C 2/15/2013 by Adam: corrected insertion of the last dummy residue
             if (dcj.eq.0) dcj=1.23591524223
              c(j,i)=c(j,i-1)+dcj
              c(j,nres+i)=c(j,i)
+             dC(j,i)=c(j,i)
            enddo     
           endif   !unres_pdb
          else     !itype(i+1).eq.ntyp1
@@ -220,6 +225,7 @@ C 2/15/2013 by Adam: corrected insertion of the first dummy residue
             if (dcj.eq.0) dcj=1.23591524223
             c(j,i)=c(j,i+1)-dcj
             c(j,nres+i)=c(j,i)
+            dC(j,i)=c(j,i)
            enddo
           endif !unres_pdb
          endif !itype(i+1).eq.ntyp1
@@ -227,6 +233,7 @@ C 2/15/2013 by Adam: corrected insertion of the first dummy residue
       enddo
       write (iout,*) "After loop in readpbd"
 C Calculate the CM of the last side chain.
+      if (.not. sccalc) then
       if (unres_pdb) then
         do j=1,3
           dc(j,ires)=sccor(j,iii)
@@ -235,6 +242,7 @@ C Calculate the CM of the last side chain.
 c        write (iout,*) "Calling sccenter iii",iii
         call sccenter(ires,iii,sccor)
       endif
+      endif
       nsup=nres
       nstart_sup=1
       if (itype(nres).ne.10) then
@@ -296,14 +304,14 @@ C Calculate internal coordinates.
       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)"
+     & "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)')
+        write (iout,'(a3,1x,i4,3f8.3,5x,3f8.3)')
      &    restyp(itype(ires)),ires,(c(j,ires),j=1,3),
      &    (c(j,ires+nres),j=1,3)
       enddo
-      endif
       call flush(iout)
+      endif
 c      write(iout,*)"before int_from_cart nres",nres
       call int_from_cart(.true.,.false.)
       do i=1,nres
@@ -338,9 +346,9 @@ C Copy the coordinates to reference coordinates
       enddo
   100 format (//'              alpha-carbon coordinates       ',
      &          '     centroid coordinates'/
-     1          '       ', 6X,'X',11X,'Y',11X,'Z',
+     1          '       ', 7X,'X',11X,'Y',11X,'Z',
      &                          10X,'X',11X,'Y',11X,'Z')
-  110 format (a,'(',i3,')',6f12.5)
+  110 format (a,'(',i4,')',6f12.5)
 cc enddiag
       do j=1,nbfrag     
         do i=1,4                                                       
@@ -636,9 +644,9 @@ C Calculate internal coordinates.
       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)"
+     & "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)') 
+        write (iout,'(a3,1x,i4,3f8.3,5x,3f8.3)') 
      &    restyp(itype(ires)),ires,(c(j,ires),j=1,3),
      &    (c(j,ires+nres),j=1,3)
       enddo

diff --git a/source/unres/src-HCD-5D/readpdb.F b/source/unres/src-HCD-5D/readpdb.F
index 1ffc884..1190bb1 100644 (file)
--- a/source/unres/src-HCD-5D/readpdb.F
+++ b/source/unres/src-HCD-5D/readpdb.F
@@ -585,9 +585,9 @@ C Calculate internal coordinates.
       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)"
+     & "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)') 
+        write (iout,'(a3,1x,i4,3f8.3,5x,3f8.3)') 
      &    restyp(itype(ires)),ires,(c(j,ires),j=1,3),
      &    (c(j,ires+nres),j=1,3)
       enddo

diff --git a/source/unres/src-HCD-5D/readrtns_CSA.F b/source/unres/src-HCD-5D/readrtns_CSA.F
index 0320484..c51e45e 100644 (file)
--- a/source/unres/src-HCD-5D/readrtns_CSA.F
+++ b/source/unres/src-HCD-5D/readrtns_CSA.F
@@ -3188,6 +3188,8 @@ c    &                       constr_homology
           enddo
         lim_odl=ii
         endif
+c        write (iout,*) "Distance restraints set"
+c        call flush(iout)
 c
 c     Theta, dihedral and SC retraints
 c
@@ -3228,6 +3230,8 @@ c           sigma_dih(k,i)=sigma_dih(k,i)*sigma_dih(k,i)
           enddo
           lim_dih=nct-nnt-2 
         endif
+c        write (iout,*) "Dihedral angle restraints set"
+c        call flush(iout)
 
         if (waga_theta.gt.0.0d0) then
 c         open (ientin,file=tpl_k_sigma_theta,status='old')
@@ -3263,6 +3267,8 @@ c                             rescore(k,i-2) !  right expression ?
 c            sigma_theta(k,i)=sigma_theta(k,i)*sigma_theta(k,i)
           enddo
         endif
+c        write (iout,*) "Angle restraints set"
+c        call flush(iout)
 
         if (waga_d.gt.0.0d0) then
 c       open (ientin,file=tpl_k_sigma_d,status='old')
@@ -3298,16 +3304,23 @@ c              read (ientin,*) sigma_d(k,i) ! 1st variant
           enddo
         endif
       enddo
+c      write (iout,*) "SC restraints set"
+c      call flush(iout)
 c
 c remove distance restraints not used in any model from the list
 c shift data in all arrays
 c
+c      write (iout,*) "waga_dist",waga_dist," nnt",nnt," nct",nct
       if (waga_dist.ne.0.0d0) then
         ii=0
         liiflag=.true.
         do i=nnt,nct-2 
          do j=i+2,nct 
           ii=ii+1
+c          if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0
+c     &            .and. distal.le.dist2_cut ) then
+c          write (iout,*) "i",i," j",j," ii",ii
+c          call flush(iout)
           if (ii_in_use(ii).eq.0.and.liiflag) then
             liiflag=.false.
             iistart=ii
@@ -3332,17 +3345,23 @@ c
              enddo
              ii=ii-iishift
              lim_odl=lim_odl-iishift
+c          endif
           endif
          enddo
         enddo
       endif
-
+c      write (iout,*) "Removing distances completed"
+c      call flush(iout)
       endif ! .not. klapaucjusz
 
       if (constr_homology.gt.0) call homology_partition
+c      write (iout,*) "After homology_partition"
+c      call flush(iout)
       if (constr_homology.gt.0) call init_int_table
-c     write (iout,*) "ithet_start =",ithet_start,"ithet_end =",ithet_end
-c     write (iout,*) "loc_start =",loc_start,"loc_end =",loc_end
+c      write (iout,*) "After init_int_table"
+c      call flush(iout)
+c      write (iout,*) "ithet_start =",ithet_start,"ithet_end =",ithet_end
+c      write (iout,*) "loc_start =",loc_start,"loc_end =",loc_end
 c
 c Print restraints
 c

diff --git a/source/unres/src-HCD-5D/stochfric.F b/source/unres/src-HCD-5D/stochfric.F
index c8a3a0d..368cf97 100644 (file)
--- a/source/unres/src-HCD-5D/stochfric.F
+++ b/source/unres/src-HCD-5D/stochfric.F
@@ -25,7 +25,7 @@
       include 'COMMON.IOUNITS'
 #ifdef FIVEDIAG
       integer iposc,ichain,n,innt,inct
-      double precision v_work(3,maxres2),vvec(maxres2_chain),rs(maxres2)
+      double precision v_work(3,maxres2),vvec(maxres2),rs(maxres2)
 #else
       double precision gamvec(MAXRES6)
       common /syfek/ gamvec

diff --git a/source/wham/src-HCD/readpdb.F b/source/wham/src-HCD/readpdb.F
index 855d754..8a85b8c 100644 (file)
--- a/source/wham/src-HCD/readpdb.F
+++ b/source/wham/src-HCD/readpdb.F
@@ -20,12 +20,13 @@ C geometry.
       integer i,j,iii,ibeg,ishift,ishift1,ity,ires,ires_old
       double precision dcj
       integer rescode,kkk,lll,icha,cou,kupa,iprzes
-      logical lsecondary
+      logical lsecondary,sccalc
       integer iterter(maxres)
       double precision efree_temp
       iii=0
       ibeg=1
       ishift1=0
+      sccalc=.false.
       do
         read (ipdbin,'(a80)',end=10) card
 !       write (iout,'(a)') card
@@ -66,11 +67,13 @@ C geometry.
             call sccenter(ires,iii,sccor)
           endif
           iii=0
+          sccalc=.true.
         endif
 ! 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  
+          sccalc=.false.
           read (card(12:16),*) atom
 c          write (2,'(a)') card
 !          write (iout,*) "! ",atom," !",ires
@@ -94,6 +97,7 @@ c          write (2,'(a)') card
                 call sccenter(ires_old,iii,sccor)
               endif
               iii=0
+              sccalc=.true.
             endif
 ! Start new residue.
             if (res.eq.'Cl-' .or. res.eq.'Na+') then
@@ -214,7 +218,7 @@ C          endif !unres_pdb
         endif  !itype.eq.ntyp1
       enddo
 C Calculate the CM of the last side chain.
-      call sccenter(ires,iii,sccor)
+      if (.not. sccalc) call sccenter(ires,iii,sccor)
       nsup=nres
       nstart_sup=1
       if (itype(nres).ne.10) then