A bunch of utility scripts for the VMD visualization software.

Note: below is given a summary of each script. However, refer to the source file for documentation.

You can use Git software for revision control to download an updatable version of this repository. If you don't have it, install it by following the instructions at this site. Once you have it working, go to a terminal and type:

cd ../path-to-create-a-copy
git clone https://github.com/franciscoadasme/vmdtools.git

This will generate a vmdtools folder at the current location, which is under revision control. To update your local copy of the repository, execute

git pull

in your directory to fetch and merge remote changes.

1. Click the Code green button in the repository webpage, and then Download ZIP inside the popup window.
2. Extract the files into a folder.

To update your local copy, you have to download it again and replace the older files.

Most VMD scripts are written in the Tcl language and they usually define a bunch of functions that should be imported into the VMD session by invoking the following:

source <script>.tcl

Some scripts have command-line interface (indicated below), which can be also run as follows:

vmd -dispdev none -e <script>.tcl -args ARG1 ARG2 ARG3 ...

The documentation of command-line arguments can be read in the header of the script file.

Defines utility functions built upon VMD [measure hbonds ...] command to detect h-bonds and water bridges in a structure and trajectory. H-bonds are detected between two atom selections, which may be mediated by water molecules. The residues (identified by their resindex) involved in h-bonds are reported instead of individual atoms for better trackability, as atoms that form h-bonds may change during the trajectory, especially when waters are involved.

There are three main functions:

• hbond_search for finding h-bonds in a single structure
• hbond_traj for finding h-bonds in a trajectory
• hbond_traj_table for printing out a table of residues involved in h-bonds in a trajectory

The following is an example of finding h-bonds in a trajectory and printing the h-bond table into a comma-separated value (.csv) file:

mol new system.pdb
mol addfile traj.dcd
set sel [atomselect top "resname LIG and resid 1"]
set other [atomselect top "protein"]
lassign [hbond_traj $sel $other -waters 2] residues hbonds
set output [open hbonds.csv w]
hbond_traj_table $output $residues $hbonds
close $output

Note that hbond_search and hbond_traj accept optional arguments (e.g., -waters) for controlling how h-bonds are detected. Refer to the script file for more information.

Be sure to thank these contributors:

• franciscoadasme Francisco Adasme - creator, maintainer
• maurobedoya Mauricio Bedoya - contributor

Licensed under the MIT license, see the separate LICENSE file.