trj_parch.py Command Help
Command: $SCHRODINGER/run trj_parch.py
usage: trj_parch.py [-h] [-output-trajectory-format {auto,dtr,xtc}]
[-s START:END:STEP] [-ref-mae <file>] [-ref-asl <ASL>]
[-align-asl <ASL>] [-center-only] -dew-asl <ASL>
[-nwaters <int>] [-n <int>] [-fep-lambda {0,1}]
[-protein-fep]
cms trj out
This program edits a given trajectory as follows:
1. Align each frame to a reference structure as specified via the -ref-mae
option. If this option is not specified, the one from the input CMS file
will be used as the reference structure. The atoms to align can be
specified via the -align-asl option. If it is not specified, the program
will select the atoms automatically based on the following precedences
from high to low:
A. For protein or covalent-ligand FEP systems, the backbone of the mutated
residues will be selected for alignment.
B. If protein is present in the system, all backbone atoms will be selected
for alignment.
C. If it is a FEP system for the solvent leg, the core atoms will be
selected for alignment.
D. If it is a FEP system for the solvent leg, but there are no core atoms
it will be treated as if an absolute binding job and atoms marked
with ABSOLUTE_BINDING_LIGAND will be selected for alignment.
E. All solute atoms will be selected for alignment.
Note that the value of -align-asl will be applied to both the reference
structure and each trajectory frame. If you wish to use a different
atom selection for the reference structure only, you can specify that via
the -ref-asl option.
In any cases, the atoms selected in both the reference structure and each
trajectory frame should match each other. If selected atoms include protein
backbone atoms, all non-backbone atoms will be ignored.
2. For each frame, remove the solvent molecules beyond the region of interest,
which is herein referred to as the 'dew point' and can be specified via
the -dew-asl option. The number of solvent molecules to retain can be
specified via the -n option.
3. In the case of FEP system, atoms corresponding to the other end point will
also be removed.
The default number of solvent molecules retained by this script is 200. This is
approximately the number of water molecules in a spherical droplet of radius
11.5 Ångstroms at the temperature of 300 K. 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(Å): 7.2 9.1 11.5 13.0 14.3 15.4 16.4 17.3 18.0 18.8 19.6
positional arguments:
cms Input .cms file name
trj Input trajectory file or dir name, which typically
ends with an extension name of '.xtc' (XTC format) or
'_trj' (DTR format), e.g., jobname.xtc, jobname_trj
out Output file basename
options:
-h, --help show this help message and exit
-output-trajectory-format {auto,dtr,xtc}
Specify the output trajectory's format. Default: auto,
which means the same format as the input trajectory.
-s START:END:STEP, -slice-trj START:END:STEP
Use the sliced trajectory. We use Python's slice
notation. START, END, and STEP should be integer
numbers.
-ref-mae <file> Reference structure file in either .cms or .mae format
If not specified, the default reference structure will
be that from the <cms> argument.
-ref-asl <ASL> ASL expression to select atoms in the reference
structure. If not specified, the same ASL expression
as that of -align-asl will be evaluated against the
reference structure to get the reference coordinates.
-align-asl <ASL> ASL expression to select atoms in each trajectory
frame. The atoms selected in each frame will be
aligned to atoms in the reference structure selected
by -ref-asl. If not specified, the program will select
atoms automatically (see this module's description.)
-center-only Skip the alignment steps, and instead just center the
entire system on the -dew-asl selection
-dew-asl <ASL> ASL expression to specify the atoms around which a
solvent droplet ('dew') will be retained. (Required)
-nwaters <int> (DEPRECATED! Please use -n instead.)
-n <int> Number of solvent molecules to keep. Default: 200
-fep-lambda {0,1} Specify the FEP lambda end point to keep.
-protein-fep (DEPRECATED! This option has no effects now. The
program will automatically detect if it is a protein
FEP system or not.)