VMD TopoTools package. Version 1.8

This package contains contributed features from:

Josh Vermaas (fully working gromacs topology files for CHARMM)
Konstantin W (replicatemols for non-orthogonal cells)

Overview

TopoTools is a plugin for VMD providing a collection of Tcl commands to manipulate, build, read and write topologies (i.e. bonds, angles, dihedrals, etc. and their corresponding properties (type, order, etc.).

Updates

Updated and bugfix versions are also available from: http://sites.google.com/site/akohlmey/software/topotools and: https://github.com/akohlmey/topotools That page also links to tutorials demonstrating the use of the package for different purposes.

TODO

improve "topo setbonds" to be more efficient for large sets of bonds to be added.
topo copybonds
topo guessbonds (use bondsrecalc and restore bonds outside the selection)
support for generating and replicating bonds across periodic boundaries (for molecular crystal models).
better documentation, more tutorials
more tools to read/write custom topology files (e.g. gromacs top?, amber parmtop?)
API to read/parse/store force field database information.

Installation

TopoTools is written entirely in the Tcl scripting language for use as a plugin with VMD. A version of TopoTools is already bundled with VMD, to update it with the newer, downloaded version unpack the TopoTools archive, which will create a directory containing that various Tcl script files. If the directory is not named topotools1.8, please rename it. Now, find the plugin folder in your VMD installation where it already has a topotools1.x directory and move the folder with the new version next to it. If it already has the topotools1.8 folder, overwrite the files inside with the new version. VMD should use the new version automatically at the next start.

Feedback

Please report any problems, bugs, suggestions, inquiries or code contributions to the github hosted SCM page at: https://github.com/akohlmey/topotools/issues