TopoTools-v1.1 has been released with VMD version 1.9. Key features: first public version, basic support for listing, typing, adding, and removing bonds, angles, dihedrals, and impropers, read/write support for LAMMPS data files, periodic system replication, merging of "VMD molecules" to a single molecule, merging of selections. TopoTools-v1.0 has been released together with VMD version 1.8.7. Please cite TopoTools as: Axel Kohlmeyer, (2017).
#VMD TOPOTOOLS HOW TO#
Learn how to use TopoTools from the on-line tutorial. Please file bug reports and feature requests as GitHub issues. This should return the version number of the plugin that you have installed. To find out which version of topotools you have, please open the VMD text mode console and type: package require topotools. TopoTools consists of a generic middleware script layer that makes access to the topology related data stored in VMD more convenient than the existing very basic API, but it also has a number of high-level tools that allow reading and writing of topology file formats that cannot be parsed by the molfile plugins (as they need additional information not available to molfile plugins), parsing of parameter and residue database files for generation of complete input files for MD codes like LAMMPS and HOOMD-blue, and replicating or combining multiple systems (i.e.
It is meant to be a complementary tool to psfgen, which is very much optimized for building topologies for biomolecules.
TopoTools is a VMD plugin for manipulating topology information.
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