schrodinger.application.desmond.packages.parch module

This script handles both MD and FEP trajectories with the following modifications:
  1. For each frame, remove the water molecules beyond the region of interest, which is herein referred to as ‘dew point’ as specified by -dew-asl option. To ensure that the output trajectory contains the same number of atoms, we set the waters to retain to a fixed number. Number of waters to keep is specified by -nwaters option.
  2. Align each frame to a reference structure, specified by the -ref-mae
    option. If this is not specified, align the frames on the input CMS file.
  3. Remove dummy atoms when FEP trajectories are provided. The user must specify the lambda-window {0 or 1} of interest through the -fep-lambda option.

The script was designed to handle all virtual sites used by OPLS3e and in TIP4P water model.

The default number of water molecules retained by this script is 200. This is approximately the number of waters in a spherical droplet of radius 11.5 Angstroms (300K). To estimate the number of water molecules to retain, use this table:

nWat: 50 100 200 300 400 500 600 700 800 900 1000 r(A): 7.2 9.1 11.5 13.0 14.3 15.4 16.4 17.3 18.0 18.8 19.6
schrodinger.application.desmond.packages.parch.get_bb_ordered_aids(st, asl)

This function returns a list of aids for protein backbone, ordered by connectivity of the polypeptide chain (N->C terminus). This is important for Protein-FEP jobs as the mutated residue is added to the end of the atom list. :rtype: list of int

schrodinger.application.desmond.packages.parch.reset_solvent_resnum(cms_model: Cms) → None

Change water residue number from 1 to the maximum parched value.

schrodinger.application.desmond.packages.parch.main(argv=None)