TopoTools is a VMD plugin for manipulating topology information. It is meant to be a complementary tool to psfgen, which is very much optimized for building topologies for biomolecules. 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. VMD "molecules"). Learn how to use TopoTools from the on-line tutorial. Version HistoryVersion 1.0TopoTools-v1.0 has been released together with VMD version 1.8.7. Version 1.1TopoTools-v1.1 has been released with VMD version 1.9. Version 1.2The final version of TopoTools-v1.2 has been released with VMD version 1.9.1.This version contains important bugfixes in - Sanity check on atom coordinate data when reading lammps data files. - Initial implementation for topo guessbonds (only works on "all" selections).- Bugfixes in topo readvarxyz (safer format checking, no spurious empty frames)- Bugfixes in topo guessatom (can handle element/type/name fields with unusual characters)topo writegmxtop (doesn't create charge groups with more than 32 atoms, better atom indexing)- Bugfixes in topo readlammpsdata (can handle data files with class2 coefficients, doesn't writes topology information (bonds, angles, dihedrals, impropers) compatible with atom style)- Bugfixes in topo writelammpsdata (use resid instead of residue property, as basis for molecule ids, since this is what we read in)Version 1.3The version of TopoTools-v1.3 was distributed with alpha test versions of VMD version 1.9.2.This version contains bugfixes and improvements to reduce the stack space requirements when operating on large systems with over 500,000 atoms. Special thanks to John Stone and Michael Doig for bringing this to my attention and explanations why this happens and how this can be avoided. New features:- Reduced stack space requirements - Support for writing non-orthogonal cells - Better detection of unknown topo subcommands - Better detection for insufficient data when parsing the Atoms section in LAMMPS data files - Consistent behavior when guessing bonds after reading them through molfile rather than from within topotools script - Support for reading PairIJ Coeff section (ignored like all Coeff sections currently) Version 1.4The final version of TopoTools-v1.4 scheduled to be released with VMD version 1.9.2.This version contains bugfixes and improvements and adds support for accessing crossterms contributed by Josh Vermaas. This feature requires a version of VMD newer than 1.9.2a33, but version 1.4 should also work with older versions of VMD; only the crossterm support will not function correctly. New features:- A new utility function TopoTools::fixupnumtypes which prepends numerical atom/bond/angle/etc types with leading zeros so they get sorted consistently and in the correct numerical order with ascii style sorting. This facilitates maintaining the order of numerical atom/bond/angle/etc types, e.g. when reading and writing data files from LAMMPS. Installationunpack the tar archive which will create a directory named topotools1.4, and move it next to the topotools1.x directory from your existing VMD 1.9.1 installation. VMD should use the new version automatically at the next start. To uninstall, just remove the topotools1.4 directory.
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