Client No Solvent¶
Welcome to
_________ _______ _______ _______ _ _______ ______
\__ __/( ___ )|\ /|( ____ )( ____ \( ( /|( )( __ \
) ( | ( ) || ) ( || ( )|| ( \/| \ ( || () () || ( \ )
| | | (___) || | | || (____)|| (__ | \ | || || || || | ) |
| | | ___ || | | || __)| __) | (\ \) || |(_)| || | | |
| | | ( ) || | | || (\ ( | ( | | \ || | | || | ) |
| | | ) ( || (___) || ) \ \__| (____/\| ) \ || ) ( || (__/ )
)_( |/ \|(_______)|/ \__/(_______/|/ )_)|/ \|(______/
A command-line interface for Molecular Dynamics Analysis routines.
version: 0.11.2
Remove solvent from trajectory.¶
Algorithm¶
Removes solvent from trajectory using MDTraj.remove_solvent.
Examples¶
Remove all solvent:
taurenmd nosol top.pdb traj.dcd -d traj_nosol.dcd -o
Remove all solvent except for NA atoms:
taurenmd nosol top.pdb traj.dcd -d traj_nosolNA.dcd -e Na -o
tmdnosol
can be used as main command:
tmdnosol [...]
References¶
MD data accessed and/or processed using MDTraj
usage: tmdnosol [-h] [-v] [-i] [-d TRAJ_OUTPUT] [-o [TOP_OUTPUT]]
[-m MAINTAIN [MAINTAIN ...]]
topology trajectories [trajectories ...]
Positional Arguments¶
- topology
Path to the topology file.
- trajectories
Path to the trajectory files. If multiple files are given, trajectories will be concatenated by input order.
Named Arguments¶
- -v, --version
show program’s version number and exit
- -i, --insort
Sorts input trajectories paths according to their tail numbers, if paths are formatted as follows: my_trajectory_#.dcd, where # is a number. Defaults to
False
.Default: False
- -d, --traj-output
Modified trajectory output file name. File type will be defined by file name extension. Defaults to traj_out.dcd.
Default: “traj_out.dcd”
- -o, --top-output
Export edited trajectory first frame as topololy file. You can specify the exact file name, otherwise, defaults to input trajectory path + ‘frame0.pdb’. Also, if name starts with ‘’, it is used as file suffix, if name ends with ‘_’, it is used as prefix, instead.
Default: False
- -m, --maintain
List of solvent residue names to maintain in trajectory. Feeds MDTraj.Trajectory.remove_solvent.exclude parameter.