8/11/12 by Adam: fixed disulfide bridge problems

Conflicts:

	bin/unres/CSA/unres_csa_ifort_mpich-1.2.7p1.exe
	bin/unres/MD-M/unres_Tc_procor_oldparm_em64-D-symetr.exe
	bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe
	bin/unres/MD/unres_ifort_MPICH_GAB.exe
	bin/unres/MD/unres_ifort_single_GAB.exe
	source/unres/src_MD/parmread.F

diff --git a/bin/unres/CSA/unres_csa_ifort_mpich-1.2.7p1.exe b/bin/unres/CSA/unres_csa_ifort_mpich-1.2.7p1.exe
deleted file mode 100755 (executable)
index fca8c0a..0000000
Binary files a/bin/unres/CSA/unres_csa_ifort_mpich-1.2.7p1.exe and /dev/null differ

diff --git a/bin/unres/MD-M/unres_Tc_procor_oldparm_em64-D-symetr.exe b/bin/unres/MD-M/unres_Tc_procor_oldparm_em64-D-symetr.exe
deleted file mode 100755 (executable)
index 1674d45..0000000
Binary files a/bin/unres/MD-M/unres_Tc_procor_oldparm_em64-D-symetr.exe and /dev/null differ

diff --git a/bin/unres/MD/unres_ifort_MPICH_GAB.exe b/bin/unres/MD/unres_ifort_MPICH_GAB.exe
deleted file mode 100755 (executable)
index 1801713..0000000
Binary files a/bin/unres/MD/unres_ifort_MPICH_GAB.exe and /dev/null differ

diff --git a/source/unres/src_CSA/Makefile b/source/unres/src_CSA/Makefile
index 74b5dd0..ae3faf7 120000 (symlink)
--- a/source/unres/src_CSA/Makefile
+++ b/source/unres/src_CSA/Makefile
@@ -1 +1 @@
-Makefile-DFA-NEWPARM.piasek
\ No newline at end of file
+Makefile_GAB
\ No newline at end of file

diff --git a/source/unres/src_MD-M/energy_p_new_barrier.F b/source/unres/src_MD-M/energy_p_new_barrier.F
index a954c33..dee7c2f 100644 (file)
--- a/source/unres/src_MD-M/energy_p_new_barrier.F
+++ b/source/unres/src_MD-M/energy_p_new_barrier.F
@@ -387,14 +387,14 @@ cMS$ATTRIBUTES C ::  proc_proc
 #ifdef SPLITELE
       etot=wsc*evdw+wscp*evdw2+welec*ees+wvdwpp*evdw1
      & +wang*ebe+wtor*etors+wscloc*escloc
-     & +wstrain*ehpb+nss*ebr+wcorr*ecorr+wcorr5*ecorr5
+     & +wstrain*ehpb+wcorr*ecorr+wcorr5*ecorr5
      & +wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3
      & +wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d
      & +wbond*estr+Uconst+wsccor*esccor
 #else
       etot=wsc*evdw+wscp*evdw2+welec*(ees+evdw1)
      & +wang*ebe+wtor*etors+wscloc*escloc
-     & +wstrain*ehpb+nss*ebr+wcorr*ecorr+wcorr5*ecorr5
+     & +wstrain*ehpb+wcorr*ecorr+wcorr5*ecorr5
      & +wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3
      & +wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d
      & +wbond*estr+Uconst+wsccor*esccor
@@ -4126,7 +4126,7 @@ c      dscj_inv=dsc_inv(itypj)
       cosphi=om12-om1*om2
       eij=akcm*deltad*deltad+akth*(deltat1*deltat1+deltat2*deltat2)
      &  +akct*deltad*deltat12
-     &  +v1ss*cosphi+v2ss*cosphi*cosphi+v3ss*cosphi*cosphi*cosphi
+     &  +v1ss*cosphi+v2ss*cosphi*cosphi+v3ss*cosphi*cosphi*cosphi+ebr
 c      write(iout,*) i,j,"rij",rij,"d0cm",d0cm," akcm",akcm," akth",akth,
 c     &  " akct",akct," deltad",deltad," deltat",deltat1,deltat2,
 c     &  " deltat12",deltat12," eij",eij 

diff --git a/source/unres/src_MD/Makefile_single_ifort b/source/unres/src_MD/Makefile_single_ifort
index bc66bba..245206b 100644 (file)
--- a/source/unres/src_MD/Makefile_single_ifort
+++ b/source/unres/src_MD/Makefile_single_ifort
@@ -37,7 +37,7 @@ object = unres.o arcos.o cartprint.o chainbuild.o convert.o initialize_p.o \
         cored.o rmdd.o geomout.o readpdb.o regularize.o thread.o fitsq.o mcm.o \
         mc.o bond_move.o refsys.o check_sc_distr.o check_bond.o contact.o djacob.o \
         eigen.o blas.o add.o entmcm.o minim_mcmf.o \
-        MP.o compare_s1.o prng_32.o \
+        MP.o compare_s1.o prng.o \
         banach.o rmsd.o elecont.o dihed_cons.o \
         sc_move.o local_move.o \
         intcartderiv.o lagrangian_lesyng.o\

diff --git a/source/unres/src_MD/energy_p_new_barrier.F b/source/unres/src_MD/energy_p_new_barrier.F
index 64dd328..8a9a3eb 100644 (file)
--- a/source/unres/src_MD/energy_p_new_barrier.F
+++ b/source/unres/src_MD/energy_p_new_barrier.F
@@ -428,14 +428,14 @@ cMS$ATTRIBUTES C ::  proc_proc
 #ifdef SPLITELE
       etot=wsc*evdw+wscp*evdw2+welec*ees+wvdwpp*evdw1
      & +wang*ebe+wtor*etors+wscloc*escloc
-     & +wstrain*ehpb+nss*ebr+wcorr*ecorr+wcorr5*ecorr5
+     & +wstrain*ehpb+wcorr*ecorr+wcorr5*ecorr5
      & +wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3
      & +wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d
      & +wbond*estr+Uconst+wsccor*esccor
 #else
       etot=wsc*evdw+wscp*evdw2+welec*(ees+evdw1)
      & +wang*ebe+wtor*etors+wscloc*escloc
-     & +wstrain*ehpb+nss*ebr+wcorr*ecorr+wcorr5*ecorr5
+     & +wstrain*ehpb+wcorr*ecorr+wcorr5*ecorr5
      & +wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3
      & +wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d
      & +wbond*estr+Uconst+wsccor*esccor
@@ -1057,25 +1057,25 @@ C------------------------------------------------------------------------
      &  edihcnstr,ebr*nss,
      &  Uconst,etot
    10 format (/'Virtual-chain energies:'//
-     & 'EVDW=  ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/
-     & 'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/
-     & 'EES=   ',1pE16.6,' WEIGHT=',1pD16.6,' (p-p)'/
-     & 'EVDWPP=',1pE16.6,' WEIGHT=',1pD16.6,' (p-p VDW)'/
-     & 'ESTR=  ',1pE16.6,' WEIGHT=',1pD16.6,' (stretching)'/
-     & 'EBE=   ',1pE16.6,' WEIGHT=',1pD16.6,' (bending)'/
-     & 'ESC=   ',1pE16.6,' WEIGHT=',1pD16.6,' (SC local)'/
-     & 'ETORS= ',1pE16.6,' WEIGHT=',1pD16.6,' (torsional)'/
-     & 'ETORSD=',1pE16.6,' WEIGHT=',1pD16.6,' (double torsional)'/
-     & 'EHPB=  ',1pE16.6,' WEIGHT=',1pD16.6,
+     & 'EVDW=  ',1pE16.6,' WEIGHT=',1pE16.6,' (SC-SC)'/
+     & 'EVDW2= ',1pE16.6,' WEIGHT=',1pE16.6,' (SC-p)'/
+     & 'EES=   ',1pE16.6,' WEIGHT=',1pE16.6,' (p-p)'/
+     & 'EVDWPP=',1pE16.6,' WEIGHT=',1pE16.6,' (p-p VDW)'/
+     & 'ESTR=  ',1pE16.6,' WEIGHT=',1pE16.6,' (stretching)'/
+     & 'EBE=   ',1pE16.6,' WEIGHT=',1pE16.6,' (bending)'/
+     & 'ESC=   ',1pE16.6,' WEIGHT=',1pE16.6,' (SC local)'/
+     & 'ETORS= ',1pE16.6,' WEIGHT=',1pE16.6,' (torsional)'/
+     & 'ETORSD=',1pE16.6,' WEIGHT=',1pE16.6,' (double torsional)'/
+     & 'EHPB=  ',1pE16.6,' WEIGHT=',1pE16.6,
      & ' (SS bridges & dist. cnstr.)'/
-     & 'ECORR4=',1pE16.6,' WEIGHT=',1pD16.6,' (multi-body)'/
-     & 'ECORR5=',1pE16.6,' WEIGHT=',1pD16.6,' (multi-body)'/
-     & 'ECORR6=',1pE16.6,' WEIGHT=',1pD16.6,' (multi-body)'/
-     & 'EELLO= ',1pE16.6,' WEIGHT=',1pD16.6,' (electrostatic-local)'/
-     & 'ETURN3=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 3rd order)'/
-     & 'ETURN4=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 4th order)'/
-     & 'ETURN6=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 6th order)'/
-     & 'ESCCOR=',1pE16.6,' WEIGHT=',1pD16.6,' (backbone-rotamer corr)'/
+     & 'ECORR4=',1pE16.6,' WEIGHT=',1pE16.6,' (multi-body)'/
+     & 'ECORR5=',1pE16.6,' WEIGHT=',1pE16.6,' (multi-body)'/
+     & 'ECORR6=',1pE16.6,' WEIGHT=',1pE16.6,' (multi-body)'/
+     & 'EELLO= ',1pE16.6,' WEIGHT=',1pE16.6,' (electrostatic-local)'/
+     & 'ETURN3=',1pE16.6,' WEIGHT=',1pE16.6,' (turns, 3rd order)'/
+     & 'ETURN4=',1pE16.6,' WEIGHT=',1pE16.6,' (turns, 4th order)'/
+     & 'ETURN6=',1pE16.6,' WEIGHT=',1pE16.6,' (turns, 6th order)'/
+     & 'ESCCOR=',1pE16.6,' WEIGHT=',1pE16.6,' (backbone-rotamer corr)'/
      & 'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/
      & 'ESS=   ',1pE16.6,' (disulfide-bridge intrinsic energy)'/
      & 'UCONST= ',1pE16.6,' (Constraint energy)'/ 
@@ -4424,7 +4424,7 @@ c      dscj_inv=dsc_inv(itypj)
       deltat12=om2-om1+2.0d0
       cosphi=om12-om1*om2
       eij=akcm*deltad*deltad+akth*(deltat1*deltat1+deltat2*deltat2)
-     &  +akct*deltad*deltat12
+     &  +akct*deltad*deltat12+ebr
      &  +v1ss*cosphi+v2ss*cosphi*cosphi+v3ss*cosphi*cosphi*cosphi
 c      write(iout,*) i,j,"rij",rij,"d0cm",d0cm," akcm",akcm," akth",akth,
 c     &  " akct",akct," deltad",deltad," deltat",deltat1,deltat2,

diff --git a/source/unres/src_MD/initialize_p.F b/source/unres/src_MD/initialize_p.F
index a99edfc..565ccaf 100644 (file)
--- a/source/unres/src_MD/initialize_p.F
+++ b/source/unres/src_MD/initialize_p.F
@@ -1377,6 +1377,7 @@ c------------------------------------------------------------------------------
       include 'COMMON.IOUNITS'
       include 'COMMON.SETUP'
       include 'COMMON.CONTROL'
+c      write(2,*)"hpb_partition: nhpb=",nhpb
 #ifdef MPI
       call int_bounds(nhpb,link_start,link_end)
       if (.not. out1file) 
@@ -1388,5 +1389,6 @@ c------------------------------------------------------------------------------
       link_start=1
       link_end=nhpb
 #endif
+c      write(2,*)"hpb_partition: link_start=",nhpb," link_end=",link_end
       return
       end

diff --git a/source/unres/src_MD/parmread.F b/source/unres/src_MD/parmread.F
index bdc3809..62a0ddf 100644 (file)
--- a/source/unres/src_MD/parmread.F
+++ b/source/unres/src_MD/parmread.F
@@ -557,26 +557,26 @@ C Read of Side-chain backbone correlation parameters
 C Modified 11 May 2012 by Adasko
 CCC
 C
-      read (isccor,*,end=119,err=119) nsccortyp
-      read (isccor,*,end=119,err=119) (isccortyp(i),i=1,ntyp)
+      read (isccor,*,end=1113,err=1113) nsccortyp
+      read (isccor,*,end=1113,err=1113) (isccortyp(i),i=1,ntyp)
 c      write (iout,*) 'ntortyp',ntortyp
       maxinter=3
 cc maxinter is maximum interaction sites
       do l=1,maxinter    
       do i=1,nsccortyp
        do j=1,nsccortyp
-         read (isccor,*,end=119,err=119) nterm_sccor(i,j),nlor_sccor(i,j)
+         read (isccor,*,end=1113,err=1113) nterm_sccor(i,j),nlor_sccor(i,j)
           v0ijsccor=0.0d0
           si=-1.0d0
   
          do k=1,nterm_sccor(i,j)
-           read (isccor,*,end=119,err=119) kk,v1sccor(k,l,i,j)
+           read (isccor,*,end=1113,err=1113) kk,v1sccor(k,l,i,j)
      &    ,v2sccor(k,l,i,j) 
             v0ijsccor=v0ijsccor+si*v1sccor(k,l,i,j)
             si=-si
           enddo
          do k=1,nlor_sccor(i,j)
-            read (isccor,*,end=119,err=119) kk,vlor1sccor(k,i,j),
+            read (isccor,*,end=1113,err=1113) kk,vlor1sccor(k,i,j),
      &        vlor2sccor(k,i,j),vlor3sccor(k,i,j) 
             v0ijsccor=v0ijsccor+vlor1sccor(k,i,j)/
      &(1+vlor3sccor(k,i,j)**2)
@@ -965,6 +965,9 @@ c      v3ss=0.0d0
       goto 999
   113 write (iout,*) "Error reading torsional energy parameters."
       goto 999
+ 1113 write (iout,*) 
+     &  "Error reading side-chain torsional energy parameters."
+      goto 999
   114 write (iout,*) "Error reading double torsional energy parameters."
       goto 999
   115 write (iout,*) 

diff --git a/source/unres/src_MD/readrtns.F b/source/unres/src_MD/readrtns.F
index c5dc889..10cde78 100644 (file)
--- a/source/unres/src_MD/readrtns.F
+++ b/source/unres/src_MD/readrtns.F
@@ -1127,8 +1127,8 @@ czscore          call geom_to_var(nvar,coord_exp_zs(1,1))
 c        write (iout,*) "constr_dist",constr_dist,nstart_sup,nsup
       if (constr_dist.gt.0) then
         call read_dist_constr
-        call hpb_partition
       endif
+      if (nhpb.gt.0) call hpb_partition
 c      write (iout,*) "After read_dist_constr nhpb",nhpb
 c      call flush(iout)
       if (indpdb.eq.0 .and. modecalc.ne.2 .and. modecalc.ne.4