pyqmmm.md.amber_toolkit

A library of CPPTraj scripts and built-in generator functions.

Functions

angles_and_dist_script(protein_id, h_index, ...)	Get distances and angles
basic_metrics_script(protein_id, ...)	Get basic useful metrics
calculate_hbonds_script(protein_id, ...)	Calculate all hbonds that form between the protein and substrate.
closest_waters_script(protein_id, centroid, ...)	Extract the 9000 waters closest to the centroid
gbsa_script(protein_id, ligand_name, ...[, cpus])	Submit a GBSA calculation.
get_last_frame(prmtop, mdcrd, output_pdb)	Get the last frame from a trajectory as a PDB.
run_cpptraj(cpptraj_script[, script_name])	A generalizable function that can be used to run any of the cpptraj scripts.
strip_all_script(protein_id)	Strip waters, ions, and metals and generate new mdcrd and prmtop files
submit_script(protein_id, script_name, cpus)	Classic submit script for CPPTraj jobs.