From 7007541a5b0492ff898617b0dfde67ac47230e22 Mon Sep 17 00:00:00 2001 From: Dawid Jagiela Date: Wed, 7 Mar 2012 09:18:32 -0500 Subject: [PATCH] - added input files for 2 peptides (1LE1, 1LY2) runs on matrix - minor changes in makefile and test script --- source/ga/Makefile | 4 +- source/ga/input-templates/matrix-2p/1L2Y_mremd.tpl | 14 ++ source/ga/input-templates/matrix-2p/1L2Y_wham.tpl | 46 +++++++ source/ga/input-templates/matrix-2p/1LE1_mremd.tpl | 14 ++ source/ga/input-templates/matrix-2p/1LE1_wham.tpl | 46 +++++++ source/ga/input-templates/matrix-2p/opt.csh | 69 ++++++++++ source/ga/input-templates/matrix-2p/start_all.pbs | 27 ++++ source/ga/input-templates/matrix-2p/unres_p1.csh | 26 ++++ source/ga/input-templates/matrix-2p/unres_p2.csh | 26 ++++ source/ga/input-templates/matrix-2p/unresga.inp | 7 + source/ga/input-templates/matrix-2p/wham_p1.csh | 66 ++++++++++ source/ga/input-templates/matrix-2p/wham_p2.csh | 66 ++++++++++ source/ga/input-templates/matrix-2p/zscore.tpl | 135 ++++++++++++++++++++ source/ga/tester.sh | 2 +- 14 files changed, 545 insertions(+), 3 deletions(-) create mode 100644 source/ga/input-templates/matrix-2p/1L2Y_mremd.tpl create mode 100644 source/ga/input-templates/matrix-2p/1L2Y_wham.tpl create mode 100644 source/ga/input-templates/matrix-2p/1LE1_mremd.tpl create mode 100644 source/ga/input-templates/matrix-2p/1LE1_wham.tpl create mode 100755 source/ga/input-templates/matrix-2p/opt.csh create mode 100755 source/ga/input-templates/matrix-2p/start_all.pbs create mode 100755 source/ga/input-templates/matrix-2p/unres_p1.csh create mode 100755 source/ga/input-templates/matrix-2p/unres_p2.csh create mode 100644 source/ga/input-templates/matrix-2p/unresga.inp create mode 100755 source/ga/input-templates/matrix-2p/wham_p1.csh create mode 100755 source/ga/input-templates/matrix-2p/wham_p2.csh create mode 100644 source/ga/input-templates/matrix-2p/zscore.tpl diff --git a/source/ga/Makefile b/source/ga/Makefile index 13399f6..369fb85 100644 --- a/source/ga/Makefile +++ b/source/ga/Makefile @@ -1,5 +1,5 @@ -CC := ifort +FC := ifort CFLAGS := BUILD_DIR := build @@ -13,7 +13,7 @@ CLUSTER := matrix all: checkdirs checktpl build/unresga build/unresga:GA.f - $(CC) $(CFLAGS) GA.f -o $@ + $(FC) $(CFLAGS) GA.f -o $@ checkdirs: $(BUILD_DIR) diff --git a/source/ga/input-templates/matrix-2p/1L2Y_mremd.tpl b/source/ga/input-templates/matrix-2p/1L2Y_mremd.tpl new file mode 100644 index 0000000..6fc5fce --- /dev/null +++ b/source/ga/input-templates/matrix-2p/1L2Y_mremd.tpl @@ -0,0 +1,14 @@ +1LE1 random parameters #1 +SEED=-6086648 RE pdbref refstr ONE_LETTER rescale_mode=2 out1file extconf +nstep=2000000 ntwe=10000 ntwx=10000 lang=0 tbf t_bath=300 tau_bath=1.0 & +dt=0.10 reset_moment=1000 reset_vel=10000 damax=4.0 +nrep=16 nstex=10000 tlist mlist traj1file rest1file sync nsyn=10000 tonly & +hremd={POPSIZE} + 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400 + 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +{WEIGHTS} +{PREFIX}.pdb +22 +XNLYIQWLKDGGPSSGRPPPSX +0 +0 diff --git a/source/ga/input-templates/matrix-2p/1L2Y_wham.tpl b/source/ga/input-templates/matrix-2p/1L2Y_wham.tpl new file mode 100644 index 0000000..c980249 --- /dev/null +++ b/source/ga/input-templates/matrix-2p/1L2Y_wham.tpl @@ -0,0 +1,46 @@ +SEED=-3059743 n_ene=19 isampl=1 nq=1 classify pdbref einicheck=1 & +rescale=2 ensembles=0 nslice=1 HAMIL_REP oneletter cxfile separate_parset & +nparmset={POPSIZE} +nres=22 one_letter +XNLYIQWLKDGGPSSGRPPPSX +0 +{WEIGHTS} +NT=16 replica +NR=1 TEMP= 250.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 260.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 270.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 280.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 290.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 300.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 310.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 320.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 330.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 340.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 350.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 360.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 370.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 380.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 390.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 400.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +nfile_cx=1 rec_start=101 rec_end=200 totraj=256 +./{PREFIX}_mremd_MD000 +CUTOFF_UP=8.0 CUTOFF_LOW=4.0 NLEVEL=-2 PDBREF & +SPLIT_BET=1 NC_FRAC_HEL=0.7 NC_FRAC_BET=0.5 NC_FRAC_PAIR=0.5 NSHIFT_PAIR=3 & +CONT_PAIR=1 NC_FRAC_PAIR=0.5 RMS_PAIR=0 +./{PREFIX}.pdb diff --git a/source/ga/input-templates/matrix-2p/1LE1_mremd.tpl b/source/ga/input-templates/matrix-2p/1LE1_mremd.tpl new file mode 100644 index 0000000..b36236a --- /dev/null +++ b/source/ga/input-templates/matrix-2p/1LE1_mremd.tpl @@ -0,0 +1,14 @@ +1LE1 random parameters #1 +SEED=-6086648 RE pdbref refstr ONE_LETTER rescale_mode=2 out1file extconf +nstep=2000000 ntwe=10000 ntwx=10000 lang=0 tbf t_bath=300 tau_bath=1.0 & +dt=0.10 reset_moment=1000 reset_vel=10000 damax=4.0 +nrep=16 nstex=10000 tlist mlist traj1file rest1file sync nsyn=10000 tonly & +hremd={POPSIZE} + 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400 + 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +{WEIGHTS} +{PREFIX}.pdb +14 +XSWTWENGKWTWKX +0 +0 diff --git a/source/ga/input-templates/matrix-2p/1LE1_wham.tpl b/source/ga/input-templates/matrix-2p/1LE1_wham.tpl new file mode 100644 index 0000000..f68f1e3 --- /dev/null +++ b/source/ga/input-templates/matrix-2p/1LE1_wham.tpl @@ -0,0 +1,46 @@ +SEED=-3059743 n_ene=19 isampl=1 nq=1 classify pdbref einicheck=1 & +rescale=2 ensembles=0 nslice=1 HAMIL_REP oneletter cxfile separate_parset & +nparmset={POPSIZE} +nres=14 one_letter +XSWTWENGKWTWKX +0 +{WEIGHTS} +NT=16 replica +NR=1 TEMP= 250.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 260.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 270.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 280.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 290.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 300.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 310.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 320.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 330.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 340.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 350.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 360.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 370.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 380.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 390.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +NR=1 TEMP= 400.0 FI= 0.00000 0.00000 0.00000 0.00000 0.00000 +KH= 0.00 Q0=0.00000 +nfile_cx=1 rec_start=101 rec_end=200 totraj=256 +./{PREFIX}_mremd_MD000 +CUTOFF_UP=8.0 CUTOFF_LOW=4.0 NLEVEL=-2 PDBREF & +SPLIT_BET=1 NC_FRAC_HEL=0.7 NC_FRAC_BET=0.5 NC_FRAC_PAIR=0.5 NSHIFT_PAIR=3 & +CONT_PAIR=1 NC_FRAC_PAIR=0.5 RMS_PAIR=0 +./{PREFIX}.pdb diff --git a/source/ga/input-templates/matrix-2p/opt.csh b/source/ga/input-templates/matrix-2p/opt.csh new file mode 100755 index 0000000..f8f14b5 --- /dev/null +++ b/source/ga/input-templates/matrix-2p/opt.csh @@ -0,0 +1,69 @@ +#!/bin/csh -f +# Script to run the program zscorezi_MPI on linux with MPICH (parallel version). +# + +echo "This job is running on host `hostname` " + +set DD = /users/adam/UNRES/PARAM +set BIN = /users/adam/ZSCOREZ/bin + +set POT = GB +setenv POT GB + +setenv PREFIX zscore +setenv SCRATCHDIR /tmp/`whoami` + +if ( ! -d $SCRATCHDIR ) then + mkdir $SCRATCHDIR +endif + +#hostname +#ls -l /tmp + +# +# Is the specified potential in the list of valid force fields? +# +if (($POT != "LJ") && ($POT != "LJK") && ($POT != "BP") && ($POT != "GB") \ +&& ($POT != "GBV") ) then + echo "Unknown potential type $POT" + exit(1) +endif + +# 5/17/97 parameter file assignment was changed from link to SETENV statements +# +setenv BONDPAR $DD/bond_AM1.parm +setenv THETPAR $DD/theta_abinitio.parm +setenv ROTPAR $DD/rotamers_AM1_aura.10022007.parm +#setenv BONDPAR $DD/bond.parm +#setenv THETPAR $DD/thetaml.5parm +#setenv ROTPAR $DD/scgauss.parm +setenv TORPAR $DD/torsion_631Gdp.parm +setenv TORDPAR $DD/torsion_double_631Gdp.parm +setenv ELEPAR $DD/electr_631Gdp.parm +setenv SIDEPAR $DD/scinter_${POT}.parm +setenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3 +setenv SCPPAR $DD/scp.parm +setenv SCCORPAR $DD/rotcorr_AM1.parm + +# Set parallel environment, depending on job type (interactive or batch). + +set DEBUG = 0 + +# Choose the sidechain contact function + +setenv CONTFUNC GB +if (${CONTFUNC} == "GB") then + setenv SIDEP ${DD}/contact.3.parm +else if (${CONTFUNC} == "SCDIST") then + setenv SIDEP ${DD}/cend.3.45.parm +else if (${CONTFUNC} == "CEN") then + setenv SIDEP ${DD}/cen.parm +else if (${CONTFUNC} == "ODC") then + setenv SIDEP ${DD}/odc.parm +else if (${CONTFUNC} != "SIG") then + echo "Unknown sidechain contact function ${CONTFUNC}" + exit +endif + +limit coredumpsize 0 +$BIN/zscorezMD_sccor-T-OPTERON-clust-sign-split $* diff --git a/source/ga/input-templates/matrix-2p/start_all.pbs b/source/ga/input-templates/matrix-2p/start_all.pbs new file mode 100755 index 0000000..e859950 --- /dev/null +++ b/source/ga/input-templates/matrix-2p/start_all.pbs @@ -0,0 +1,27 @@ +#PBS -N single-test +#PBS -q dque +#PBS -l nodes=32:ppn=8 +#PBS -l walltime=1:00:00 + +set NPROCS=`cat $PBS_NODEFILE | wc -l` + +cd $PBS_O_WORKDIR + +./unresga + +cat $PBS_NODEFILE|uniq > nody + +time /users/software/mpich_ssh/bin/mpirun -machinefile $PBS_NODEFILE -np $NPROCS -p4wd $PBS_O_WORKDIR $PBS_O_WORKDIR/unres_p1.csh +time /users/software/mpich_ssh/bin/mpirun -machinefile $PBS_NODEFILE -np $NPROCS -p4wd $PBS_O_WORKDIR $PBS_O_WORKDIR/unres_p2.csh + +time /users/software/mpich_ssh/bin/mpirun -machinefile $PBS_NODEFILE -np 16 -p4wd $PBS_O_WORKDIR $PBS_O_WORKDIR/wham_p1.csh +time /users/software/mpich_ssh/bin/mpirun -machinefile $PBS_NODEFILE -np 16 -p4wd $PBS_O_WORKDIR $PBS_O_WORKDIR/wham_p2.csh + +time /users/software/mpich_ssh/bin/mpirun -machinefile $PBS_NODEFILE -np 16 ./opt.csh + +set DATA=`date +%Y-%m-%d-%H%M%S` +mkdir ceiksy-$DATA +mv *.cx ceiksy-$DATA + +#mail -s "Scheraga - wyniki dla single-test sa dostepne" lightnir@gmail.com + diff --git a/source/ga/input-templates/matrix-2p/unres_p1.csh b/source/ga/input-templates/matrix-2p/unres_p1.csh new file mode 100755 index 0000000..5d5fc95 --- /dev/null +++ b/source/ga/input-templates/matrix-2p/unres_p1.csh @@ -0,0 +1,26 @@ +#!/bin/csh -f + +set DD = /users/czarek/UNRES/PARAM +#----------------------------------------------------------------------------- +setenv FGPROCS 0 +setenv POT GB +setenv PREFIX 1LE1_mremd +setenv OUT1FILE Y +#----------------------------------------------------------------------------- +setenv UNRES_BIN /users/czarek/UNRES/NEW/bin/unres_Tc_procor_new_em64_nh_hremd.exe +#----------------------------------------------------------------------------- +setenv BONDPAR $DD/bond_AM1.parm +setenv THETPAR $DD/theta_abinitio.parm +setenv ROTPAR $DD/rotamers_AM1_aura.10022007.parm +setenv TORPAR $DD/torsion_631Gdp.parm +setenv TORDPAR $DD/torsion_double_631Gdp.parm +setenv ELEPAR $DD/electr_631Gdp.parm +setenv SIDEPAR $DD/scinter_${POT}.parm +setenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3 +setenv SCPPAR $DD/scp.parm +setenv SCCORPAR $DD/rotcorr_AM1.parm +setenv PATTERN $DD/patterns.cart +#----------------------------------------------------------------------------- + +$UNRES_BIN $* + diff --git a/source/ga/input-templates/matrix-2p/unres_p2.csh b/source/ga/input-templates/matrix-2p/unres_p2.csh new file mode 100755 index 0000000..312bef9 --- /dev/null +++ b/source/ga/input-templates/matrix-2p/unres_p2.csh @@ -0,0 +1,26 @@ +#!/bin/csh -f + +set DD = /users/czarek/UNRES/PARAM +#----------------------------------------------------------------------------- +setenv FGPROCS 0 +setenv POT GB +setenv PREFIX 1L2Y_mremd +setenv OUT1FILE Y +#----------------------------------------------------------------------------- +setenv UNRES_BIN /users/czarek/UNRES/NEW/bin/unres_Tc_procor_new_em64_nh_hremd.exe +#----------------------------------------------------------------------------- +setenv BONDPAR $DD/bond_AM1.parm +setenv THETPAR $DD/theta_abinitio.parm +setenv ROTPAR $DD/rotamers_AM1_aura.10022007.parm +setenv TORPAR $DD/torsion_631Gdp.parm +setenv TORDPAR $DD/torsion_double_631Gdp.parm +setenv ELEPAR $DD/electr_631Gdp.parm +setenv SIDEPAR $DD/scinter_${POT}.parm +setenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3 +setenv SCPPAR $DD/scp.parm +setenv SCCORPAR $DD/rotcorr_AM1.parm +setenv PATTERN $DD/patterns.cart +#----------------------------------------------------------------------------- + +$UNRES_BIN $* + diff --git a/source/ga/input-templates/matrix-2p/unresga.inp b/source/ga/input-templates/matrix-2p/unresga.inp new file mode 100644 index 0000000..870fdd2 --- /dev/null +++ b/source/ga/input-templates/matrix-2p/unresga.inp @@ -0,0 +1,7 @@ +pdb=1LE1.pdb 1L2Y.pdb +alg=csa +generations=5 +cicutoff=0.01 +population=8 +whamtemplate=1LE1_wham.tpl 1L2Y_wham.tpl +mremdtemplate=1LE1_mremd.tpl 1L2Y_mremd.tpl diff --git a/source/ga/input-templates/matrix-2p/wham_p1.csh b/source/ga/input-templates/matrix-2p/wham_p1.csh new file mode 100755 index 0000000..e8fcddc --- /dev/null +++ b/source/ga/input-templates/matrix-2p/wham_p1.csh @@ -0,0 +1,66 @@ +#!/bin/csh -f +#set echo +# Script to run the program zscorezi_MPI on linux with MPICH (parallel version). +# +echo "This job is running on host `hostname` " + +set DD = /users/adam/UNRES/PARAM +set BIN = /users/adam/ZSCOREZ/bin + +set POT = GB +setenv POT GB +setenv SCRATCHDIR /tmp/`whoami` + +# +# Przygotowanie i wyczyszczenie poletka +# +if ( ! -d $SCRATCHDIR ) then + mkdir $SCRATCHDIR +endif +rm -f $SCRATCHDIR/* + +setenv PREFIX 1LE1_wham + +# +# Is the specified potential in the list of valid force fields? +# +if (($POT != "LJ") && ($POT != "LJK") && ($POT != "BP") && ($POT != "GB") \ +&& ($POT != "GBV") ) then + echo "Unknown potential type $POT" + exit(1) +endif + +# 5/17/97 parameter file assignment was changed from link to SETENV statements +# +setenv BONDPAR $DD/bond_AM1.parm +setenv THETPAR $DD/theta_abinitio.parm +setenv ROTPAR $DD/rotamers_AM1_aura.10022007.parm +setenv TORPAR $DD/torsion_631Gdp.parm +setenv TORDPAR $DD/torsion_double_631Gdp.parm +setenv ELEPAR $DD/electr_631Gdp.parm +setenv SIDEPAR $DD/scinter_${POT}.parm +setenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3 +setenv SCPPAR $DD/scp.parm +setenv SCCORPAR $DD/rotcorr_AM1.parm +setenv PATTERN $DD/patterns.cart +# Define contact function for classification +setenv CONTFUNC GB +if (${CONTFUNC} == "GB") then + setenv SIDEP ${DD}/contact.3.parm +else if (${CONTFUNC} == "SCDIST") then + setenv SIDEP ${DD}/cend.3.45.parm +else if (${CONTFUNC} == "CEN") then + setenv SIDEP ${DD}/cen.parm +else if (${CONTFUNC} == "ODC") then + setenv SIDEP ${DD}/odc.parm +else if (${CONTFUNC} != "SIG") then + echo "Unknown sidechain contact function ${CONTFUNC}" + exit +endif + +# Set parallel environment, depending on job type (interactive or batch). + +set DEBUG = 0 + +limit coredumpsize 0 +$BIN/wham_multparm-hamrep-sep $* diff --git a/source/ga/input-templates/matrix-2p/wham_p2.csh b/source/ga/input-templates/matrix-2p/wham_p2.csh new file mode 100755 index 0000000..e9081b3 --- /dev/null +++ b/source/ga/input-templates/matrix-2p/wham_p2.csh @@ -0,0 +1,66 @@ +#!/bin/csh -f +#set echo +# Script to run the program zscorezi_MPI on linux with MPICH (parallel version). +# +echo "This job is running on host `hostname` " + +set DD = /users/adam/UNRES/PARAM +set BIN = /users/adam/ZSCOREZ/bin + +set POT = GB +setenv POT GB +setenv SCRATCHDIR /tmp/`whoami` + +# +# Przygotowanie i wyczyszczenie poletka +# +if ( ! -d $SCRATCHDIR ) then + mkdir $SCRATCHDIR +endif +rm -f $SCRATCHDIR/* + +setenv PREFIX 1L2Y_wham + +# +# Is the specified potential in the list of valid force fields? +# +if (($POT != "LJ") && ($POT != "LJK") && ($POT != "BP") && ($POT != "GB") \ +&& ($POT != "GBV") ) then + echo "Unknown potential type $POT" + exit(1) +endif + +# 5/17/97 parameter file assignment was changed from link to SETENV statements +# +setenv BONDPAR $DD/bond_AM1.parm +setenv THETPAR $DD/theta_abinitio.parm +setenv ROTPAR $DD/rotamers_AM1_aura.10022007.parm +setenv TORPAR $DD/torsion_631Gdp.parm +setenv TORDPAR $DD/torsion_double_631Gdp.parm +setenv ELEPAR $DD/electr_631Gdp.parm +setenv SIDEPAR $DD/scinter_${POT}.parm +setenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3 +setenv SCPPAR $DD/scp.parm +setenv SCCORPAR $DD/rotcorr_AM1.parm +setenv PATTERN $DD/patterns.cart +# Define contact function for classification +setenv CONTFUNC GB +if (${CONTFUNC} == "GB") then + setenv SIDEP ${DD}/contact.3.parm +else if (${CONTFUNC} == "SCDIST") then + setenv SIDEP ${DD}/cend.3.45.parm +else if (${CONTFUNC} == "CEN") then + setenv SIDEP ${DD}/cen.parm +else if (${CONTFUNC} == "ODC") then + setenv SIDEP ${DD}/odc.parm +else if (${CONTFUNC} != "SIG") then + echo "Unknown sidechain contact function ${CONTFUNC}" + exit +endif + +# Set parallel environment, depending on job type (interactive or batch). + +set DEBUG = 0 + +limit coredumpsize 0 +$BIN/wham_multparm-hamrep-sep $* diff --git a/source/ga/input-templates/matrix-2p/zscore.tpl b/source/ga/input-templates/matrix-2p/zscore.tpl new file mode 100644 index 0000000..1ccc44e --- /dev/null +++ b/source/ga/input-templates/matrix-2p/zscore.tpl @@ -0,0 +1,135 @@ +iseed=3269 n_ene=19 nparmset={POPSIZE} out_newe +mask_sc=0 mask_scp=1 mask_elec=1 mask_ang=1 mask_scloc=1 mask_tor=1 & +mask_tord=1 mask_corrh=1 mask_corr5=0 mask_corr6=0 mask_el_loc=1 & +mask_turn3=1 mask_turn4=1 mask_turn6=0 mask_vdwpp=1 mask_sccor=1 +wlow_sc=0.8 wlow_scp=0.0 wlow_elec=0.00 wlow_ang=0.00 wlow_scloc=0.00 & +wlow_tor=0.0 wlow_tord=0.0 wlow_corrh=0.00 wlow_corr5=0.00 wlow_corr6=0.00 & +wlow_sccor=0.0 & +wlow_el_loc=0.00 wlow_turn3=0.00 wlow_turn4=0.00 wlow_turn6=0.00 wlow_vdwpp=0.0 +wup_sc=1.2 wup_scp=5.0 wup_elec=5.0 wup_ang=5.00 wup_scloc=5.0 & +wup_tor=5.0 wup_tord=5.0 wup_corrh=5.0 wup_corr5=5.0 wup_corr6=5.0 & +wup_el_loc=5.0 wup_turn3=5.0 wup_turn4=5.0 wup_turn6=5.0 wup_vdwpp=5.0 & +wup_sccor=0.0 +mode=3 maxmin=10 maxfun=2000 opt_mode=0 tolf=1.0E-4 rtolf=1.0E-4 out_minim & +print_ini print_fin print_stat optimize_other read_stat=4 minimizer=sumsl & +rescale_mode=2 +mod_side +end +mod_fourier +end +mod_elec +end +mod_scp +end +{WEIGHTS} +nprot=2 +{PREFIX01} +rmscut=2.0 rmscut_gap=2.0 rkt=0.01 0.01 dkt=0.01 enecut=10000 enecut_min=10000 & +enecut_max=20000 nbatch=1 nclass=2 nlevel=1 +id=coil nelem=1 mask=*.0.* +id=native nelem=1 mask=*.1.* +ngap_read=1 nT=13 beta=270 270 280 280 290 290 300 300 310 310 320 320 330 330 & +340 340 345 345 350 350 360 360 370 370 380 380 & +hefac=10000 htfac=10000 helow=0 htlow=0 +nlev1=1 nlev2=1 level1=native level2=coil +enegap=-2.0 -0.6 ewall=0.01 !270 +enegap=-2.0 -0.6 ewall=0.01 !280 +enegap=-2.0 -0.6 ewall=0.01 !290 +enegap=-2.0 -0.6 ewall=0.01 !300 +enegap=-2.0 -0.6 ewall=0.01 !310 +enegap=-2.0 -0.6 ewall=0.01 !320 +enegap=-2.0 -0.6 ewall=0.01 !330 +enegap=-2.0 -0.6 ewall=0.01 !340 +enegap=-0.5 0.5 ewall=0.01 !345 +enegap=0.5 5.0 ewall=0.01 !350 +enegap=0.5 5.0 ewall=0.01 !360 +enegap=0.5 5.0 ewall=0.01 !370 +enegap=0.5 5.0 ewall=0.01 !380 +entshanwall=3.0e9 1.0e5 3.0e9 3.0e9 3.0e9 !270 +entshanwall=3.0e9 1.0e5 3.0e9 3.0e9 3.0e9 !280 +entshanwall=3.0e9 1.0e5 3.0e9 3.0e9 3.0e9 !290 +entshanwall=3.0e9 1.0e5 3.0e9 3.0e9 3.0e9 !300 +entshanwall=3.0e9 1.0e5 3.0e9 3.0e9 3.0e9 !310 +entshanwall=3.0e9 1.0e5 3.0e9 3.0e9 3.0e9 !320 +entshanwall=3.0e9 1.0e5 3.0e9 3.0e9 3.0e9 !330 +entshanwall=3.0e9 1.0e5 3.0e9 3.0e9 3.0e9 !340 +entshanwall=3.0e9 1.0e5 3.0e9 3.0e9 3.0e9 !345 +entshanwall=3.0e9 1.0e5 3.0e9 3.0e9 3.0e9 !350 +entshanwall=3.0e9 1.0e5 3.0e9 3.0e9 3.0e9 !360 +entshanwall=3.0e9 1.0e5 3.0e9 3.0e9 3.0e9 !370 +entshanwall=3.0e9 1.0e5 3.0e9 3.0e9 3.0e9 !380 +./{PARAM01} +nres=14 one_letter +XSWTWENGKWTWKX + 0 +PDBREF CAONLY SPLIT_BET=0 print_class nfrag=1 +CUTOFF_UP=6.0 CUTOFF_LOW=6.0 RMSUP_LIM=6.0 RMSUPUP_LIM=6.0 NFRAG=1 & +FRAC_SEC=0.3 +npiece=1 n_shift1=3 n_shift2=3 rms=1 qcut=0.40 qwol=1 local=0 angcut=60.0 & +elcont=0 sccont=0 +ifrag1=2 ifrag2=13 +./{PREFIX01}.pdb +read_weights=1 +batch=1 class=all & +qlow=0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.40 0.60 0.70 0.70 0.70 & + qup=0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.90 0.90 0.90 0.90 0.90 & +wq=1.0d10 1.0d10 1.0d10 1.0d10 1.0d10 1.0d10 1.0d10 1.0d10 1.0d10 1.0d10 & +1.0d10 1.0d10 1.0d10 +end +{PREFIX02} +rmscut=2.0 rmscut_gap=2.0 rkt=0.01 0.01 dkt=0.01 enecut=10000 enecut_min=10000 & +enecut_max=20000 nbatch=1 nclass=2 nlevel=1 +id=coil nelem=1 mask=*.0.* +id=native nelem=1 mask=*.1.* +ngap_read=1 nT=13 beta=270 270 280 280 290 290 300 300 310 310 320 320 330 330 & +340 340 345 345 350 350 360 360 370 370 380 380 & +hefac=10000 htfac=10000 helow=0 htlow=0 +nlev1=1 nlev2=1 level1=native level2=coil +enegap=-2.0 -0.6 ewall=0.01 !270 +enegap=-2.0 -0.6 ewall=0.01 !280 +enegap=-2.0 -0.6 ewall=0.01 !290 +enegap=-2.0 -0.6 ewall=0.01 !300 +enegap=-2.0 -0.6 ewall=0.01 !310 +enegap=-2.0 -0.6 ewall=0.01 !320 +enegap=-2.0 -0.6 ewall=0.01 !330 +enegap=-2.0 -0.6 ewall=0.01 !340 +enegap=-0.5 0.5 ewall=0.01 !345 +enegap=0.5 5.0 ewall=0.01 !350 +enegap=0.5 5.0 ewall=0.01 !360 +enegap=0.5 5.0 ewall=0.01 !370 +enegap=0.5 5.0 ewall=0.01 !380 +entshanwall=3.0e9 1.0e5 3.0e9 3.0e9 3.0e9 !270 +entshanwall=3.0e9 1.0e5 3.0e9 3.0e9 3.0e9 !280 +entshanwall=3.0e9 1.0e5 3.0e9 3.0e9 3.0e9 !290 +entshanwall=3.0e9 1.0e5 3.0e9 3.0e9 3.0e9 !300 +entshanwall=3.0e9 1.0e5 3.0e9 3.0e9 3.0e9 !310 +entshanwall=3.0e9 1.0e5 3.0e9 3.0e9 3.0e9 !320 +entshanwall=3.0e9 1.0e5 3.0e9 3.0e9 3.0e9 !330 +entshanwall=3.0e9 1.0e5 3.0e9 3.0e9 3.0e9 !340 +entshanwall=3.0e9 1.0e5 3.0e9 3.0e9 3.0e9 !345 +entshanwall=3.0e9 1.0e5 3.0e9 3.0e9 3.0e9 !350 +entshanwall=3.0e9 1.0e5 3.0e9 3.0e9 3.0e9 !360 +entshanwall=3.0e9 1.0e5 3.0e9 3.0e9 3.0e9 !370 +entshanwall=3.0e9 1.0e5 3.0e9 3.0e9 3.0e9 !380 +./{PARAM02} +nres=22 one_letter +XNLYIQWLKDGGPSSGRPPPSX + 0 +PDBREF CAONLY SPLIT_BET=0 print_class nfrag=1 +CUTOFF_UP=6.0 CUTOFF_LOW=6.0 RMSUP_LIM=6.0 RMSUPUP_LIM=6.0 NFRAG=1 & +FRAC_SEC=0.3 +npiece=1 n_shift1=3 n_shift2=3 rms=1 qcut=0.40 qwol=1 local=0 angcut=60.0 & +elcont=0 sccont=0 +ifrag1=2 ifrag2=13 +./{PREFIX02}.pdb +read_weights=1 +batch=1 class=all & +qlow=0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.40 0.60 0.70 0.70 0.70 & + qup=0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.90 0.90 0.90 0.90 0.90 & +wq=1.0d10 1.0d10 1.0d10 1.0d10 1.0d10 1.0d10 1.0d10 1.0d10 1.0d10 1.0d10 & +1.0d10 1.0d10 1.0d10 +end +nthehel=25 ngahel=40 the0hel=70 dthehel=2 ga0hel=-100 & +nrbet=15 r0bet=3.0 nthebet=50 the0bet=60 dthebet=2 phialpha=60.0 delr=15.0 & +delb=4.0 PHIALPHA_RIGHT=47.0 PHIALPHA_LEFT=44.0 +NGRIDT=400 T0=200 DELTAT=1 diff --git a/source/ga/tester.sh b/source/ga/tester.sh index 8ac452f..253fab2 100755 --- a/source/ga/tester.sh +++ b/source/ga/tester.sh @@ -6,7 +6,7 @@ if [ -d build ]; then fi make cd build -cp -r ~/poligon/zero/* ./ +cp -r ~/poligon/first-step/* ./ ./unresga echo "" -- 1.7.9.5