Molecular modeling scripts and suchlike

This is a collection of software that I wrote and use in the course of my research, which involves molecular dynamics and other such molecular modeling techniques. If you don't know what that is, this repository is unlikely to be of interest to you.

Name		Name	Last commit message	Last commit date
Latest commit History 554 Commits
Go		Go
MMEval		MMEval
MaeTool/src		MaeTool/src
Matlab		Matlab
Perl		Perl
VinaScore		VinaScore
coulomb		coulomb
.gitignore		.gitignore
AMBER.py		AMBER.py
EasyMMPBSA.py		EasyMMPBSA.py
MMPBSA.glade		MMPBSA.glade
MMPBSA.py		MMPBSA.py
README.markdown		README.markdown
angle_over_traj.py		angle_over_traj.py
assemble_and_calc_deltag.sh		assemble_and_calc_deltag.sh
build-namd.sh		build-namd.sh
calc_fepout_deltag.sh		calc_fepout_deltag.sh
calc_protein_rmsf.py		calc_protein_rmsf.py
calc_rotamer_dihedral.py		calc_rotamer_dihedral.py
calc_ti.R		calc_ti.R
check_job_nodes.py		check_job_nodes.py
coalesce_number_list.py		coalesce_number_list.py
colorize_pdb.py		colorize_pdb.py
convert_ligand_params_to_apbs.py		convert_ligand_params_to_apbs.py
csv_stats.py		csv_stats.py
cull-waters-inside-lipid-bilayer.go		cull-waters-inside-lipid-bilayer.go
dist_over_traj.py		dist_over_traj.py
dnarna_thermo.py		dnarna_thermo.py
elecpot.py		elecpot.py
energy_breakdown.py		energy_breakdown.py
energy_correl.py		energy_correl.py
ev_animate_pdb.py		ev_animate_pdb.py
evec_pev_to_raw.py		evec_pev_to_raw.py
extract_atoms_from_pdb.py		extract_atoms_from_pdb.py
extract_correl_simulaid.py		extract_correl_simulaid.py
fepout_cat.py		fepout_cat.py
fepout_cat_legacy.py		fepout_cat_legacy.py
ffparam_charges_vs_qm.py		ffparam_charges_vs_qm.py
ffparam_dihedrals_vs_qm.py		ffparam_dihedrals_vs_qm.py
find_missing_CB.py		find_missing_CB.py
fixup_residue_by_isomorphism.py		fixup_residue_by_isomorphism.py
generate_equivalent_nbfix.py		generate_equivalent_nbfix.py
generate_fep_calc.py		generate_fep_calc.py
generate_flood.py		generate_flood.py
generate_protein_gap_restraints.py		generate_protein_gap_restraints.py
generate_zinc_finger_motif_restraints.py		generate_zinc_finger_motif_restraints.py
get_ev.py		get_ev.py
guess_pbc.py		guess_pbc.py
helix_tilt.py		helix_tilt.py
libttj.py		libttj.py
libttj.vmd.tcl		libttj.vmd.tcl
ligand_concentration.py		ligand_concentration.py
ligand_interaction.py		ligand_interaction.py
ligand_near.py		ligand_near.py
ligand_occupancy.py		ligand_occupancy.py
ligand_rotation.py		ligand_rotation.py
make_fepenergy_gnuplot.sh		make_fepenergy_gnuplot.sh
matrix_to_png.py		matrix_to_png.py
mclout_to_pdbcolors.py		mclout_to_pdbcolors.py
merge_and_label_pdfs.py		merge_and_label_pdfs.py
merge_rosetta_remodel_loops.py		merge_rosetta_remodel_loops.py
mirror		mirror
mirror-old		mirror-old
mmpbsa_decomp_to_raw.py		mmpbsa_decomp_to_raw.py
molsimfactory.py		molsimfactory.py
namd_density.py		namd_density.py
namdconf_sanity_check.py		namdconf_sanity_check.py
next_namd_prod.py		next_namd_prod.py
occupancy_overlap.py		occupancy_overlap.py
parse_idws_fepout.py		parse_idws_fepout.py
pdb_to_psf.py		pdb_to_psf.py
plot-bend-angle.gnuplot.sh		plot-bend-angle.gnuplot.sh
plot_csv_histogram.py		plot_csv_histogram.py
plot_idws_fepout.py		plot_idws_fepout.py
plot_many_columns.py		plot_many_columns.py
plot_many_feps.py		plot_many_feps.py
plot_namd_benchmarks.py		plot_namd_benchmarks.py
polarize-martini-waters.py		polarize-martini-waters.py
psf_chargesum.py		psf_chargesum.py
psf_prm_to_bin.py		psf_prm_to_bin.py
psf_to_rtf.py		psf_to_rtf.py
qfree		qfree
regenerate_psf.py		regenerate_psf.py
relentless_fep.py		relentless_fep.py
remap_coorvel.py		remap_coorvel.py
renumber_psf_pdb.py		renumber_psf_pdb.py
reorder_pdb_and_mdcrd.py		reorder_pdb_and_mdcrd.py
resid_map.py		resid_map.py
rosetta_loopmodeling_remodel_blueprint.py		rosetta_loopmodeling_remodel_blueprint.py
sjobs		sjobs
slurm-resume		slurm-resume
slurm-suspend		slurm-suspend
softcore_setup.py		softcore_setup.py
submit-g09.sh		submit-g09.sh
submit-g16.sh		submit-g16.sh
submit-sequential		submit-sequential
sum.py		sum.py
sum_ti.py		sum_ti.py
textmatrix_to_mcl.py		textmatrix_to_mcl.py
unwrap_dcd.sh		unwrap_dcd.sh

ttjoseph/mmdevel

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