From: Adam Liwo Date: Thu, 8 Nov 2012 13:58:32 +0000 (-0500) Subject: 8/11/12 by Adam: fixed disulfide bridge problems X-Git-Tag: v.3.2~17 X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=commitdiff_plain;h=e123f68beb7954771018d0311468c68250b5f2d1 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 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 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 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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