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run.007a.cartesian_min.csh
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run.007a.cartesian_min.csh
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#!/bin/tcsh -fe
#
# After docking all of the ligands from the library to the grid, minimize and rescore each of them
# in Cartesian space.
#
### Set some variables manually
set attractive = "6"
set repulsive = "12"
### Set some paths
set dockdir = "${DOCKHOMEWORK}/bin"
set amberdir = "${AMBERHOMEWORK}/bin"
set moedir = "${MOEHOMEWORK}/bin"
set rootdir = "${VS_ROOTDIR}"
set mpidir = "${VS_MPIDIR}/bin"
set masterdir = "${rootdir}/zzz.master"
set paramdir = "${rootdir}/zzz.parameters"
set scriptdir = "${rootdir}/zzz.scripts"
set zincdir = "${rootdir}/zzz.zinclibs"
set system = "${VS_SYSTEM}"
set vendor = "${VS_VENDOR}"
### Choose parameters for cluster
### LIRED 24 ppn
### SeaWulf 28 ppn
### Rizzo 24 ppn
set wcl = 48:00:00
set nodes = 4
set ppn = 28
set queue = "long"
@ numprocs = (${nodes} * ${ppn})
### Make the appropriate directory. If it already exists, remove previous dock results from only
### the same vendor.
if (! -e ${rootdir}/${system}/007.cartesian-min) then
mkdir -p ${rootdir}/${system}/007.cartesian-min/
endif
rm -rf ${rootdir}/${system}/007.cartesian-min/${vendor}
mkdir -p ${rootdir}/${system}/007.cartesian-min/${vendor}
cd ${rootdir}/${system}/007.cartesian-min/${vendor}
### Count the number of chunks
set num_chunks = `ls -l ${rootdir}/${system}/005.zinclibs/${vendor}/ | grep chunk | grep mol2 | wc -l`
echo "num_chunks = ${num_chunks}"
set chunk = "0"
echo "Concatenating all of the chunks together..."
### Iterate over each chunk, concatenate them together
while (${chunk} < ${num_chunks})
if ( -e ${rootdir}/${system}/006.dock-to-grid/${vendor}/chunk${chunk}/${vendor}.${chunk}.output_scored.mol2 ) then
cat ${rootdir}/${system}/006.dock-to-grid/${vendor}/chunk${chunk}/${vendor}.${chunk}.output_scored.mol2 >> input.mol2
else
echo "Could not find an output mol2 file in ${rootdir}/${system}/006.dock-to-grid/${vendor}/${chunk}"
endif
@ chunk++
end
### Cat on the leftover chunk, if it exists
if ( -e ${rootdir}/${system}/006.dock-to-grid/${vendor}/leftover/${vendor}.leftover.output_scored.mol2 ) then
cat ${rootdir}/${system}/006.dock-to-grid/${vendor}/leftover/${vendor}.leftover.output_scored.mol2 >> input.mol2
endif
### Minimize the reference ligand position in the context of the receptor
echo "Minimizing reference ligand..."
##################################################
cat <<EOF >${system}.${vendor}.reference_minimization.in
conformer_search_type rigid
use_internal_energy yes
internal_energy_rep_exp 12
internal_energy_cutoff 100
ligand_atom_file ${rootdir}/${system}/001.lig-prep/${system}.lig.python.mol2
limit_max_ligands no
skip_molecule no
read_mol_solvation no
calculate_rmsd yes
use_rmsd_reference_mol yes
rmsd_reference_filename ${rootdir}/${system}/001.lig-prep/${system}.lig.python.mol2
use_database_filter no
orient_ligand no
bump_filter no
score_molecules yes
contact_score_primary no
contact_score_secondary no
grid_score_primary no
grid_score_secondary no
multigrid_score_primary no
multigrid_score_secondary no
dock3.5_score_primary no
dock3.5_score_secondary no
continuous_score_primary yes
continuous_score_secondary no
cont_score_rec_filename ${rootdir}/${system}/002.rec-prep/${system}.rec.clean.mol2
cont_score_att_exp ${attractive}
cont_score_rep_exp ${repulsive}
cont_score_rep_rad_scale 1
cont_score_use_dist_dep_dielectric yes
cont_score_dielectric 4.0
cont_score_vdw_scale 1
cont_score_es_scale 1
footprint_similarity_score_secondary no
pharmacophore_score_score_secondary no
descriptor_score_secondary no
gbsa_zou_score_secondary no
gbsa_hawkins_score_secondary no
SASA_score_secondary no
amber_score_secondary no
minimize_ligand yes
simplex_max_iterations 1000
simplex_tors_premin_iterations 0
simplex_max_cycles 1
simplex_score_converge 0.1
simplex_cycle_converge 1.0
simplex_trans_step 1.0
simplex_rot_step 0.1
simplex_tors_step 10.0
simplex_random_seed 0
simplex_restraint_min yes
simplex_coefficient_restraint 5.0
atom_model all
vdw_defn_file ${paramdir}/vdw_AMBER_parm99.defn
flex_defn_file ${paramdir}/flex.defn
flex_drive_file ${paramdir}/flex_drive.tbl
ligand_outfile_prefix output
write_orientations no
num_scored_conformers 1
rank_ligands no
EOF
##################################################
### Execute dock on the headnode
${dockdir}/dock6 -i ${system}.${vendor}.reference_minimization.in -o ${system}.${vendor}.reference_minimization.out
mv output_scored.mol2 ${system}.lig.python.min.mol2
### Write footprints for multigrids later
###########################################################################################
cat <<EOF >${system}.footprint_rescore.in
conformer_search_type rigid
use_internal_energy no
ligand_atom_file ${system}.lig.python.min.mol2
limit_max_ligands no
skip_molecule no
read_mol_solvation no
calculate_rmsd no
use_database_filter no
orient_ligand no
bump_filter no
score_molecules yes
contact_score_primary no
contact_score_secondary no
grid_score_primary no
grid_score_secondary no
multigrid_score_primary no
multigrid_score_secondary no
dock3.5_score_primary no
dock3.5_score_secondary no
continuous_score_primary no
continuous_score_secondary no
footprint_similarity_score_primary yes
footprint_similarity_score_secondary no
fps_score_use_footprint_reference_mol2 yes
fps_score_footprint_reference_mol2_filename ${system}.lig.python.min.mol2
fps_score_foot_compare_type Euclidean
fps_score_normalize_foot no
fps_score_foot_comp_all_residue no
fps_score_choose_foot_range_type threshold
fps_score_vdw_threshold 0.5
fps_score_es_threshold 0.2
fps_score_hb_threshold 0.5
fps_score_use_remainder yes
fps_score_receptor_filename ${rootdir}/${system}/002.rec-prep/${system}.rec.clean.mol2
fps_score_vdw_att_exp 6
fps_score_vdw_rep_exp 12
fps_score_vdw_rep_rad_scale 1
fps_score_use_distance_dependent_dielectric yes
fps_score_dielectric 4.0
fps_score_vdw_fp_scale 1
fps_score_es_fp_scale 1
fps_score_hb_fp_scale 0
pharmacophore_score_secondary no
descriptor_score_secondary no
gbsa_zou_score_secondary no
gbsa_hawkins_score_secondary no
SASA_score_secondary no
amber_score_secondary no
minimize_ligand no
atom_model all
vdw_defn_file ${paramdir}/vdw_AMBER_parm99.defn
flex_defn_file ${paramdir}/flex.defn
flex_drive_file ${paramdir}/flex_drive.tbl
ligand_outfile_prefix output
write_footprints yes
write_hbonds no
write_orientations no
num_scored_conformers 1
rank_ligands no
EOF
#################################################
### Create primary residues dat file
${dockdir}/dock6 -i ${system}.footprint_rescore.in -o ${system}.footprint_rescore.out
cp ${system}.footprint_rescore.out footprint_rescore.out
###########################################################################################
grep -A 1 "range_union" footprint_rescore.out | grep -v "range_union" | grep -v "\-" | sed -e '{s/,/\n/g}' | sed -e '{s/ //g}' | sed '/^$/d' | sort -n | uniq > temp.dat
foreach i ("`cat temp.dat`")
printf "%0*d\n" 3 $i >> primary_residues.dat
end
foreach r ("`cat temp.dat`")
grep " $r " output_footprint_scored.txt | awk -v temp=$r '{if ($2 == temp) print $0;}' | awk '{print $1 " " $3 " " $4}' >> reference.txt
end
grep "remainder" output_footprint_scored.txt | sed -e '{s/,/ /g}' | tr -d '\n' | awk '{print $2 " " $3 " " $6}' >> reference.txt
rm temp.dat
cp output_footprint_scored.txt ${system}.footprint.txt
#EOF
###########################################################################################
cp primary_residues.dat ${system}.primary_residues.dat
mv reference.txt ${system}.reference.txt
### Write the dock.in file
##################################################
cat <<EOF >${system}.${vendor}.cartesian_min.in
conformer_search_type rigid
use_internal_energy yes
internal_energy_rep_exp 12
internal_energy_cutoff 100.0
ligand_atom_file input.mol2
limit_max_ligands no
skip_molecule no
read_mol_solvation no
calculate_rmsd no
use_database_filter no
orient_ligand no
bump_filter no
score_molecules yes
contact_score_primary no
contact_score_secondary no
grid_score_primary no
grid_score_secondary no
multigrid_score_primary no
multigrid_score_secondary no
dock3.5_score_primary no
dock3.5_score_secondary no
continuous_score_primary yes
continuous_score_secondary no
cont_score_rec_filename ${rootdir}/${system}/002.rec-prep/${system}.rec.clean.mol2
cont_score_att_exp ${attractive}
cont_score_rep_exp ${repulsive}
cont_score_rep_rad_scale 1
cont_score_use_dist_dep_dielectric yes
cont_score_dielectric 4.0
cont_score_vdw_scale 1
cont_score_es_scale 1
footprint_similarity_score_secondary no
pharmacophore_score_secondary no
descriptor_score_secondary no
gbsa_zou_score_secondary no
gbsa_hawkins_score_secondary no
SASA_score_secondary no
amber_score_secondary no
minimize_ligand yes
simplex_max_iterations 1000
simplex_tors_premin_iterations 0
simplex_max_cycles 1
simplex_score_converge 0.1
simplex_cycle_converge 1.0
simplex_trans_step 1.0
simplex_rot_step 0.1
simplex_tors_step 10.0
simplex_random_seed 0
simplex_restraint_min yes
simplex_coefficient_restraint 5.0
atom_model all
vdw_defn_file ${paramdir}/vdw_AMBER_parm99.defn
flex_defn_file ${paramdir}/flex.defn
flex_drive_file ${paramdir}/flex_drive.tbl
ligand_outfile_prefix ${vendor}.output
write_orientations no
num_scored_conformers 1
rank_ligands no
EOF
##################################################
### Write the Cluster submit file
##################################################
if (`hostname -f` == "login1.cm.cluster" || `hostname -f` == "login2.cm.cluster" ) then
cat <<EOF >${system}.${vendor}.cartesian_min.qsub.csh
#!/bin/tcsh
#PBS -l walltime=${wcl}
#PBS -l nodes=${nodes}:ppn=${ppn}
#PBS -N ${system}.${vendor}.cartmin
#PBS -V
#PBS -q ${queue}
cd ${rootdir}/${system}/007.cartesian-min/${vendor}/
${mpidir}/mpirun -np ${numprocs} \
${dockdir}/dock6.mpi -v \
-i ${system}.${vendor}.cartesian_min.in \
-o ${system}.${vendor}.cartesian_min.out
EOF
##################################################
### Write the Cluster submit file
##################################################
###if (`hostname -f` == "rizzo.cm.cluster")
else
cat <<EOF >${system}.${vendor}.cartesian_min.qsub.csh
#!/bin/tcsh
#SBATCH --time=${wcl}
#SBATCH --nodes=${nodes}
#SBATCH --ntasks=24
#SBATCH --job-name=${system}.${vendor}.cartmin
#SBATCH --output=${system}.${vendor}.cartmin
#SBATCH -p rn-long
cd ${rootdir}/${system}/007.cartesian-min/${vendor}/
${mpidir}/mpirun -np ${numprocs} \
${dockdir}/dock6.mpi -v \
-i ${system}.${vendor}.cartesian_min.in \
-o ${system}.${vendor}.cartesian_min.out
EOF
endif
##################################################
### Submit the job
echo "Submitting ${system}.${vendor}.cartesian_min "
qsub ${system}.${vendor}.cartesian_min.qsub.csh > & ${system}.${vendor}.cartesian_min.qsub.log
date
exit