gencom

  • This command is employed after executing PaCS-MD.
  • The COMs of a selected atom group from a trajectory (generated by "gencom traj") or multiple trajectories in one trial of PaCS-MD (generated by "gencom trial") can be computed and outputted in pdb format.
  • The COMs are stored as a VIRTUAL SITE in the pdb file.
  • This command visualizes the migration paths of atoms and supports intuitive interpretation.

gencom traj

  • This command is used after executing PaCS-MD.
  • The COMs of a selected atom group from a trajectory file can be calculated and outputted in pdb format.
  • This command visualizes the migration paths of atoms and supports intuitive interpretation.

Example

  • The following example generates a pathway file pathway.pdb that contains the COMs of ligand from the prd.xtc file.
pacs gencom traj mdtraj -trj ./trial001/cycle001/replica001/prd.xtc -top ./inputs/input.gro -s "resname ligand"

Arguments

usage: pacs gencom traj mdtraj [-h] [-trj] [-top] [-s] [-r] [-o]
  • -trj, --trajectory (str):
    • trajectory file path (e.g. -trj best_complete_fit.xtc)
  • -top, --top_mdtraj (str):
    • topology file path for mdtraj (e.g. -s ./trial001/cycle000/replica001/rmmol_top.pdb)
  • -s, --selection (str):
    • atom selection for visualization (e.g. -s "resname ligand")
  • -r, --resid (int):
    • Index of the visualized center of mass on the output pdb (e.g. -r 1)
    • default: 1
  • -o, --output (str):
    • output file path (e.g. -o pathway.pdb)
    • default: pathway.pdb

gencom trial

  • This command is used after executing PaCS-MD.
  • The COMs of a selected atom group from all of the trajectories within one trial of PaCS-MD can be calculated and outputted in pdb format.
  • This command visualizes the migration paths of atoms and supports intuitive interpretation.

Example

  • The following example generates a pathway file pathway.pdb that saves the COMs of ligand from prd_fit.xtc file in the trial 1.
pacsmd gencom trial mdtraj -t 1 -trj prd_fit.xtc -top ./inputs/input.gro -s "resname ligand"

Arguments

usage: pacs gencom trial mdtraj [-h] [-t] [-trj] [-top] [-s] [-r] [-o] [-sf]
  • -t, --trial (int):
    • trial number without 0-fill when pacsmd was conducted (e.g. -t 1)
  • -trj, --trajectory (str):
    • trajectory file name (e.g. -trj prd_rmmol_fit.xtc)
  • -top, --top_mdtraj (str):
    • topology file path for mdtraj (e.g. -s ./trial001/cycle000/replica001/rmmol_top.pdb)
  • -s, --selection (str):
    • atom selection for ligand (e.g. -s "resname ligand")
  • -r, --resid (int):
    • Index of the visualized center of mass on the output pdb (e.g. -r 1)
    • default: 1
  • -o, --output (str):
    • output file path (e.g. -o pathway.pdb)
    • default: pathway.pdb
  • -sf, --stride_frame (int):
    • stride to skip when extracting the com for visualization (e.g. -sf 10)
    • default: 10