Adam's changes from nostromo to wham with homology

diff --git a/source/wham/src/COMMON.CONTROL b/source/wham/src/COMMON.CONTROL
index ed0f98b..209c22a 100644 (file)
--- a/source/wham/src/COMMON.CONTROL
+++ b/source/wham/src/COMMON.CONTROL
@@ -1,6 +1,6 @@
       integer iscode,indpdb,outpdb,outmol2,icomparfunc,pdbint,
      & ensembles,constr_dist,constr_homology,homol_nset,
-     & iset
+     & iset,ihset
       real*8 waga_homology
       real*8 waga_dist, waga_angle, waga_theta, waga_d, dist_cut
       logical refstr,pdbref,punch_dist,print_rms,caonly,verbose,
@@ -11,5 +11,5 @@
      & merge_helices,bxfile,cxfile,histfile,entfile,zscfile,rmsrgymap,
      & ensembles,with_dihed_constr,check_conf,histout,constr_dist,
      & constr_homology,out1file,homol_nset
-      common /homol/  waga_homology(MaxProcs/20),
-     & waga_dist,waga_angle,waga_theta,waga_d,dist_cut,iset
+      common /homol/  waga_homology(maxR),
+     & waga_dist,waga_angle,waga_theta,waga_d,dist_cut,iset,ihset

diff --git a/source/wham/src/COMMON.PROTFILES b/source/wham/src/COMMON.PROTFILES
index 3287326..d758573 100644 (file)
--- a/source/wham/src/COMMON.PROTFILES
+++ b/source/wham/src/COMMON.PROTFILES
@@ -1,4 +1,4 @@
-      character*80 protfiles(maxfile_prot,2,MaxR,MaxT_h,Max_Parm),
+      character*128 protfiles(maxfile_prot,2,MaxR,MaxT_h,Max_Parm),
      &  bprotfiles
       integer nfile_bin(MaxR,MaxT_h,Max_Parm),
      &  nfile_asc(MaxR,MaxT_h,Max_Parm),

diff --git a/source/wham/src/DIMENSIONS.FREE b/source/wham/src/DIMENSIONS.FREE
index 7d5a31e..85a618f 100644 (file)
--- a/source/wham/src/DIMENSIONS.FREE
+++ b/source/wham/src/DIMENSIONS.FREE
@@ -4,7 +4,7 @@
       integer MaxSlice
       parameter (Max_Parm=32)
       parameter (MaxQ=4,MaxQ1=MaxQ+2)
-      parameter(MaxR=8,MaxT_h=32)
+      parameter(MaxR=32,MaxT_h=32)
       parameter(MaxSlice=40)
       integer MaxN
       parameter (MaxN=100)

diff --git a/source/wham/src/bxread.F b/source/wham/src/bxread.F
index bebf420..112d8ca 100644 (file)
--- a/source/wham/src/bxread.F
+++ b/source/wham/src/bxread.F
@@ -20,7 +20,8 @@
       include "COMMON.FREE"
       include "COMMON.SBRIDGE"
       real*4 csingle(3,maxres2)
-      character*64 nazwa,bprotfile_temp
+      character*64 nazwa
+      character*128 bprotfile_temp
       character*3 liczba
       integer i,is,ie,j,ii,jj,k,kk,l,ll,mm,if,m
       integer nrec,nlines,iscor,islice

diff --git a/source/wham/src/contact.f b/source/wham/src/contact.f
index 5b05d57..f6909dd 100644 (file)
--- a/source/wham/src/contact.f
+++ b/source/wham/src/contact.f
@@ -2,6 +2,7 @@
       implicit none
       include 'DIMENSIONS'
       include 'DIMENSIONS.ZSCOPT'
+      include 'DIMENSIONS.FREE'
       include 'COMMON.CONTROL'
       include 'COMMON.IOUNITS'
       include 'COMMON.CHAIN'

diff --git a/source/wham/src/cxread.F b/source/wham/src/cxread.F
index 5c6d751..d7dcbf8 100644 (file)
--- a/source/wham/src/cxread.F
+++ b/source/wham/src/cxread.F
@@ -18,7 +18,8 @@
       include 'COMMON.VAR'
       include 'COMMON.GEO'
       include 'COMMON.PROT'
-      character*64 nazwa,bprotfile_temp
+      character*64 nazwa
+      character*128 bprotfile_temp
       real*4 rtime,rpotE,ruconst,rt_bath,rprop(maxQ)
       double precision time
       integer iret,itmp,itraj,ntraj

diff --git a/source/wham/src/define_pairs.f b/source/wham/src/define_pairs.f
index 00866a8..789575b 100644 (file)
--- a/source/wham/src/define_pairs.f
+++ b/source/wham/src/define_pairs.f
@@ -3,6 +3,7 @@
       include 'DIMENSIONS'
       include 'DIMENSIONS.ZSCOPT'
       include 'DIMENSIONS.COMPAR'
+      include 'DIMENSIONS.FREE'
       include 'COMMON.IOUNITS'
       include 'COMMON.TIME1'
       include 'COMMON.SBRIDGE'

diff --git a/source/wham/src/enecalc1.F b/source/wham/src/enecalc1.F
index 3d878ad..7f6f8d7 100644 (file)
--- a/source/wham/src/enecalc1.F
+++ b/source/wham/src/enecalc1.F
@@ -46,7 +46,7 @@
       double precision tt
       integer snk_p(MaxR,MaxT_h,Max_parm)
       logical lerr
-      character*64 bprotfile_temp
+      character*128 bprotfile_temp
       integer scount_t(0:maxprocs-1)
       call opentmp(islice,ientout,bprotfile_temp)
       iii=0
@@ -165,10 +165,10 @@ c     &   " kfac",kfac,"quot",quot," fT",fT
      &      wtor_d,wsccor,wbond
 #endif
         call etotal(energia(0),fT)
-        if (constr_homology) energia(0)=energia(0)+
+        if (constr_homology.gt.0) energia(0)=energia(0)+
      &   waga_homology(iset)*energia(22)
-        write (iout,*) "constr_homology",constr_homology," iset",iset,
-     &   " waga_homology",waga_homology(iset)
+c        write (iout,*) "constr_homology",constr_homology," iset",iset,
+c     &   " waga_homology",waga_homology(iset)
 #ifdef DEBUG
         write (iout,*) "Conformation",i
         call enerprint(energia(0),fT)
@@ -219,6 +219,8 @@ c        call pdbout(ii+1,beta_h(ib,ipar),efree,energia(0),0.0d0,rmsdev)
      &         1.0d0/(1.987D-3*beta_h(ib,ipar))
 #ifdef DEBUG
              call enerprint(energia(0),fT)
+#endif
+#ifdef DEBUG
              write (iout,'(4f10.5,2i5)') 0.0,energia(0),0.0,
      &       1.0d0/(beta_h(ib,ipar)*1.987D-3),
      &       0,0

diff --git a/source/wham/src/energy_p_new.F b/source/wham/src/energy_p_new.F
index 5cfdcce..a954783 100644 (file)
--- a/source/wham/src/energy_p_new.F
+++ b/source/wham/src/energy_p_new.F
@@ -2,6 +2,7 @@
       implicit real*8 (a-h,o-z)
       include 'DIMENSIONS'
       include 'DIMENSIONS.ZSCOPT'
+      include 'DIMENSIONS.FREE'
 
 #ifndef ISNAN
       external proc_proc
@@ -133,7 +134,7 @@ c      write (iout,*) "ft(6)",fact(6)," evdw",evdw," evdw_t",evdw_t
      & +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4
      & +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6
      & +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d
-     & +wbond*estr+wsccor*fact(1)*esccor+ehomology_constr
+     & +wbond*estr+wsccor*fact(1)*esccor!+ehomology_constr
      & +wdfa_dist*edfadis+wdfa_tor*edfator+wdfa_nei*edfanei
      & +wdfa_beta*edfabet
 #else
@@ -144,7 +145,7 @@ c      write (iout,*) "ft(6)",fact(6)," evdw",evdw," evdw_t",evdw_t
      & +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4
      & +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6
      & +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d
-     & +wbond*estr+wsccor*fact(1)*esccor+ehomology_constr
+     & +wbond*estr+wsccor*fact(1)*esccor!+ehomology_constr
      & +wdfa_dist*edfadis+wdfa_tor*edfator+wdfa_nei*edfanei
      & +wdfa_beta*edfabet
 #endif
@@ -1820,6 +1821,7 @@ C
       implicit real*8 (a-h,o-z)
       include 'DIMENSIONS'
       include 'DIMENSIONS.ZSCOPT'
+      include 'DIMENSIONS.FREE'
       include 'COMMON.CONTROL'
       include 'COMMON.IOUNITS'
       include 'COMMON.GEO'
@@ -3149,7 +3151,7 @@ c MODELLER restraint function
       implicit real*8 (a-h,o-z)
       include 'DIMENSIONS'
       include 'DIMENSIONS.ZSCOPT'
-
+      include 'DIMENSIONS.FREE'
       integer nnn, i, j, k, ki, irec, l
       integer katy, odleglosci, test7
       real*8 odleg, odleg2, odleg3, kat, kat2, kat3, gdih(max_template)
@@ -3744,6 +3746,7 @@ c
       implicit real*8 (a-h,o-z)
       include 'DIMENSIONS'
       include 'DIMENSIONS.ZSCOPT'
+      include 'DIMENSIONS.FREE'
       include 'COMMON.LOCAL'
       include 'COMMON.GEO'
       include 'COMMON.INTERACT'
@@ -4070,6 +4073,7 @@ C
       implicit real*8 (a-h,o-z)
       include 'DIMENSIONS'
       include 'DIMENSIONS.ZSCOPT'
+      include 'DIMENSIONS.FREE'
       include 'COMMON.LOCAL'
       include 'COMMON.GEO'
       include 'COMMON.INTERACT'
@@ -4551,6 +4555,7 @@ C
       implicit real*8 (a-h,o-z)
       include 'DIMENSIONS'
       include 'DIMENSIONS.ZSCOPT'
+      include 'DIMENSIONS.FREE'
       include 'COMMON.GEO'
       include 'COMMON.LOCAL'
       include 'COMMON.VAR'
@@ -5202,6 +5207,7 @@ c        amino-acid residues.
       implicit real*8 (a-h,o-z)
       include 'DIMENSIONS'
       include 'DIMENSIONS.ZSCOPT'
+      include 'DIMENSIONS.FREE'
       include 'COMMON.VAR'
       include 'COMMON.GEO'
       include 'COMMON.LOCAL'
@@ -5596,6 +5602,10 @@ c     &         ' jj=',jj,' kk=',kk
 C Contacts I-J and (I+1)-(J+1) or (I+1)-(J-1) occur simultaneously. 
 C The system gains extra energy.
               ecorr=ecorr+ehbcorr(i,j,i+1,j1,jj,kk,0.72D0,0.32D0)
+#ifdef DEBUG
+              write (iout,*) "ecorr",i,j,i+1,j1,
+     &               ehbcorr(i,j,i+1,j1,jj,kk,0.72D0,0.32D0)
+#undef DEBUG
               n_corr=n_corr+1
             else if (j1.eq.j) then
 C Contacts I-J and I-(J+1) occur simultaneously. 
@@ -5883,11 +5893,11 @@ cd    ees0pkl=0.0D0
 cd    ees0pij=1.0D0
 cd    ees0mkl=0.0D0
 cd    ees0mij=1.0D0
-c     write (iout,*)'Contacts have occurred for peptide groups',i,j,
-c    &   ' and',k,l
-c     write (iout,*)'Contacts have occurred for peptide groups',
-c    &  i,j,' fcont:',eij,' eij',' eesij',ees0pij,ees0mij,' and ',k,l
-c    & ,' fcont ',ekl,' eeskl',ees0pkl,ees0mkl,' ees=',ees
+cd      write (iout,*)'Contacts have occurred for peptide groups',i,j,
+cd     &   ' and',k,l
+cd      write (iout,*)'Contacts have occurred for peptide groups',
+cd     &  i,j,' fcont:',eij,' eij',' eesij',ees0pij,ees0mij,' and ',k,l
+cd     & ,' fcont ',ekl,' eeskl',ees0pkl,ees0mkl,' ees=',ees
 C Calculate the multi-body contribution to energy.
       ecorr=ecorr+ekont*ees
       if (calc_grad) then

diff --git a/source/wham/src/initialize_p.F b/source/wham/src/initialize_p.F
index 0ba3b77..c1c1950 100644 (file)
--- a/source/wham/src/initialize_p.F
+++ b/source/wham/src/initialize_p.F
@@ -581,6 +581,7 @@ c------------------------------------------------------------------------------
       implicit real*8 (a-h,o-z)
       include 'DIMENSIONS'
       include 'DIMENSIONS.ZSCOPT'
+      include 'DIMENSIONS.FREE'
 #ifdef MPI
       include 'mpif.h'
 #endif

diff --git a/source/wham/src/molread_zs.F b/source/wham/src/molread_zs.F
index a736e9c..34b3210 100644 (file)
--- a/source/wham/src/molread_zs.F
+++ b/source/wham/src/molread_zs.F
@@ -5,6 +5,7 @@ C
       implicit real*8 (a-h,o-z)
       include 'DIMENSIONS'
       include 'DIMENSIONS.ZSCOPT'
+      include 'DIMENSIONS.FREE'
       include 'COMMON.IOUNITS'
       include 'COMMON.GEO'
       include 'COMMON.VAR'
@@ -353,6 +354,7 @@ c-------------------------------------------------------------------------------
       implicit real*8 (a-h,o-z)
       include 'DIMENSIONS'
       include 'DIMENSIONS.ZSCOPT'
+      include 'DIMENSIONS.FREE'
       include 'COMMON.CONTROL'
       include 'COMMON.CHAIN'
       include 'COMMON.IOUNITS'
@@ -483,6 +485,7 @@ c====-------------------------------------------------------------------
 
       include 'DIMENSIONS'
       include 'DIMENSIONS.ZSCOPT'
+      include 'DIMENSIONS.FREE'
 #ifdef MPI
       include 'mpif.h'
 #endif
@@ -532,6 +535,7 @@ c Alternative: reading from input
       call reada(controlcard,'DIST_CUT',dist_cut,5.0d0) ! for diff ways of calc sigma
  
       call readi(controlcard,"HOMOL_NSET",homol_nset,1)       
+      call readi(controlcard,"IHSET",ihset,1)       
       if (homol_nset.gt.1)then
          call card_concat(controlcard,.true.)
          read(controlcard,*) (waga_homology(i),i=1,homol_nset) 
@@ -637,7 +641,7 @@ c         write(iout,*) "tpl_k_rescore - ",tpl_k_rescore
             read (ientin,*,end=1401) rescore_tmp
 c           rescore(k,irec)=rescore_tmp+1.0d0 ! to avoid 0 values
             rescore(k,irec)=0.5d0*(rescore_tmp+0.5d0) ! alt transf to reduce scores
-c           write(iout,*) "rescore(",k,irec,") =",rescore(k,irec)
+c            write(iout,*) "rescore(",k,irec,") =",rescore(k,irec)
  1301     continue
           enddo  
  1401   continue
@@ -679,7 +683,7 @@ c             write (iout,*) "dist(",i,j,") =",dist(i,j)
 c             write (iout,*) "distal = ",distal
 c             write (iout,*) "odl(",k,ii,") =",odl(k,ii)
 c            write(iout,*) "rescore(",k,i,") =",rescore(k,i),
-c    &                      "rescore(",k,j,") =",rescore(k,j)
+c     &                      "rescore(",k,j,") =",rescore(k,j)
 c
 c  Calculation of sigma from res sim
 c
@@ -690,6 +694,7 @@ c
             if (odl(k,ii).le.dist_cut) then
               sigma_odl(k,ii)=rescore(k,i)+rescore(k,j) ! other exprs possible
 c             sigma_odl(k,ii)=hmscore(k)*rescore(k,i)*rescore(k,j)
+c              write (iout,*) "c sigma_odl",k,ii,sigma_odl(k,ii)
             else
 #ifdef OLDSIGMA
               sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))* ! sigma ~ rescore ~ error
@@ -697,6 +702,8 @@ c             sigma_odl(k,ii)=hmscore(k)*rescore(k,i)*rescore(k,j)
 #else
               sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))* ! sigma ~ rescore ~ error
      &                      dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
+c              write (iout,*) "d sigma_odl",k,ii,sigma_odl(k,ii),
+c     &           odl(k,ii),dist_cut
 #endif
 c   Following expr replaced by a positive exp argument
 c             sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
@@ -855,6 +862,7 @@ cd      write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d
      &   1.0d0/dsqrt(sigma_d(ki,i)),ki=1,constr_homology)
        enddo
       endif
+      call flush_(iout)
 c -----------------------------------------------------------------
       return
       end

diff --git a/source/wham/src/proc_cont.f b/source/wham/src/proc_cont.f
index 9269496..39ec498 100644 (file)
--- a/source/wham/src/proc_cont.f
+++ b/source/wham/src/proc_cont.f
@@ -2,6 +2,7 @@
       implicit real*8 (a-h,o-z)
       include 'DIMENSIONS'
       include 'DIMENSIONS.ZSCOPT'
+      include 'DIMENSIONS.FREE'
       include 'DIMENSIONS.COMPAR'
       include 'COMMON.IOUNITS'
       include 'COMMON.TIME1'

diff --git a/source/wham/src/promienie.f b/source/wham/src/promienie.f
index 66016fd..76923cf 100644 (file)
--- a/source/wham/src/promienie.f
+++ b/source/wham/src/promienie.f
@@ -2,6 +2,7 @@
       implicit none
       include 'DIMENSIONS'
       include 'DIMENSIONS.ZSCOPT'
+      include 'DIMENSIONS.FREE'
       include 'COMMON.CONTROL'
       include 'COMMON.INTERACT'
       include 'COMMON.IOUNITS'

diff --git a/source/wham/src/read_ref_str.F b/source/wham/src/read_ref_str.F
index 4b56181..72e1a47 100644 (file)
--- a/source/wham/src/read_ref_str.F
+++ b/source/wham/src/read_ref_str.F
@@ -6,6 +6,7 @@ C
       implicit none
       include 'DIMENSIONS'
       include 'DIMENSIONS.ZSCOPT'
+      include 'DIMENSIONS.FREE'
       include 'DIMENSIONS.COMPAR'
       include 'COMMON.IOUNITS'
       include 'COMMON.GEO'

diff --git a/source/wham/src/readpdb.F b/source/wham/src/readpdb.F
index e90d954..ca900d3 100644 (file)
--- a/source/wham/src/readpdb.F
+++ b/source/wham/src/readpdb.F
@@ -4,6 +4,7 @@ C geometry.
       implicit real*8 (a-h,o-z)
       include 'DIMENSIONS'
       include 'DIMENSIONS.ZSCOPT'
+      include 'DIMENSIONS.FREE'
       include 'COMMON.FRAG'
       include 'COMMON.LOCAL'
       include 'COMMON.VAR'
@@ -290,6 +291,7 @@ c---------------------------------------------------------------------------
       implicit real*8 (a-h,o-z)
       include 'DIMENSIONS'
       include 'DIMENSIONS.ZSCOPT'
+      include 'DIMENSIONS.FREE'
 #ifdef MPI
       include "mpif.h"
 #endif
@@ -392,6 +394,7 @@ c-------------------------------------------------------------------------------
       implicit real*8 (a-h,o-z)
       include 'DIMENSIONS'
       include 'DIMENSIONS.ZSCOPT'
+      include 'DIMENSIONS.FREE'
 #ifdef MPI
       include "mpif.h"
 #endif

diff --git a/source/wham/src/readrtns.F b/source/wham/src/readrtns.F
index bc964f3..3d308b4 100644 (file)
--- a/source/wham/src/readrtns.F
+++ b/source/wham/src/readrtns.F
@@ -252,7 +252,7 @@ c-----------------------------------------------------------------------------
       include "COMMON.NAMES"
       include "COMMON.FREE"
       include "COMMON.OBCINKA"
-      character*64 nazwa
+      character*128 nazwa
       character*16000 controlcard
       integer i,ii,ib,iR,iparm,ilen,iroof,nthr,npars
       external ilen,iroof
@@ -355,7 +355,7 @@ c-------------------------------------------------------------------------------
       include "COMMON.PROTFILES"
       include "COMMON.PROT"
       include "COMMON.FREE"
-      character*64 bprotfile_temp
+      character*128 bprotfile_temp
       character*3 liczba,liczba2
       character*2 liczba1
       integer iunit,islice
@@ -415,7 +415,8 @@ c-------------------------------------------------------------------------------
       include "COMMON.SBRIDGE"
       include "COMMON.OBCINKA"
       real*4 csingle(3,maxres2)
-      character*64 nazwa,bprotfile_temp
+      character*64 nazwa
+      character*128 bprotfile_temp
       character*3 liczba
       character*2 liczba1
       integer i,j,ii,jj(maxslice),k,kk(maxslice),l,

diff --git a/source/wham/src/secondary.f b/source/wham/src/secondary.f
index 9c9bc7d..1d194ab 100644 (file)
--- a/source/wham/src/secondary.f
+++ b/source/wham/src/secondary.f
@@ -2,6 +2,7 @@
       implicit real*8 (a-h,o-z)
       include 'DIMENSIONS'
       include 'DIMENSIONS.ZSCOPT'
+      include 'DIMENSIONS.FREE'
       include 'DIMENSIONS.COMPAR'
       include 'COMMON.IOUNITS'
       include 'COMMON.TIME1'

diff --git a/source/wham/src/wham_calc1.F b/source/wham/src/wham_calc1.F
index 300bb86..ce5de23 100644 (file)
--- a/source/wham/src/wham_calc1.F
+++ b/source/wham/src/wham_calc1.F
@@ -696,7 +696,7 @@ c              write (iout,*) 1.0d0/(beta_h(ib,iparm)*1.987D-3),ft
             edihcnstr=enetb(20,i,iparm)
             ehomology_constr=enetb(22,i,iparm)
             if (homol_nset.gt.1) 
-     &       ehomology_constr=waga_homology(homol_nset)*ehomology_constr
+     &       ehomology_constr=waga_homology(ihset)*ehomology_constr
             edfadis=enetb(23,i,iparm)
             edfator=enetb(24,i,iparm)
             edfanei=enetb(25,i,iparm)
@@ -956,7 +956,7 @@ c      write (iout,*) "me1",me1," scount",scount(me1)
           edihcnstr=enetb(20,t,iparm)
           ehomology_constr=enetb(22,t,iparm)
           if (homol_nset.gt.1)
-     &       ehomology_constr=waga_homology(homol_nset)*ehomology_constr
+     &       ehomology_constr=waga_homology(ihset)*ehomology_constr
           edfadis=enetb(23,t,iparm)
           edfator=enetb(24,t,iparm)
           edfanei=enetb(25,t,iparm)

diff --git a/source/wham/src/xread.F b/source/wham/src/xread.F
index ac35de1..9e5efb9 100644 (file)
--- a/source/wham/src/xread.F
+++ b/source/wham/src/xread.F
@@ -23,7 +23,8 @@
       include "COMMON.SBRIDGE"
       include "COMMON.OBCINKA"
       real*4 csingle(3,maxres2)
-      character*64 nazwa,bprotfile_temp
+      character*64 nazwa
+      character*128 bprotfile_temp
       integer i,j,k,l,ii,jj(maxslice),kk(maxslice),ll(maxslice),
      &  mm(maxslice)
       integer iscor,islice,islice1,slice