Skip to content
/ mmdevel Public

Molecular modeling scripts and things

7 stars 4 forks Branches Tags Activity
Star
Notifications You must be signed in to change notification settings

ttjoseph/mmdevel

BranchesTags

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

563 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
 
 
clustal_to_html.py
clustal_to_html.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
 
 

Repository files navigation

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.

About

Molecular modeling scripts and things

Resources

Readme
Activity

Stars

7 stars

Watchers

1 watching

Forks

4 forks
Report repository

Releases

1 tags

Packages

No packages published

Languages