Recent site activity

  • TclMPI
    attachment removed by Axel Kohlmeyer
    attachment from Axel Kohlmeyer
    edited by Axel Kohlmeyer
  • VRPN-ICMS
    edited by Axel Kohlmeyer
  • TclMPI
    edited by Axel Kohlmeyer
  • LAMMPS-ICMS
    edited by Axel Kohlmeyer
  • TclMPI
    attachment from Axel Kohlmeyer
  • View All
Software‎ > ‎

TopoTools

Contents

  1. 1 Version History
    1. 1.1 Version 1.0
    2. 1.2 Version 1.1
    3. 1.3 Version 1.2
    4. 1.4 Version 1.3
  2. 2 Installation

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 History

Version 1.0

TopoTools-v1.0 has been released together with VMD version 1.8.7.
 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.

Version 1.1

TopoTools-v1.1 has been released with VMD version 1.9.
Several bugfixes, especially for operating on selections and assigning atom properties.
New features:
- determination of angle and dihedral definitions from bonding information.
- guess of impropers. searches for atoms bound to exactly three other atoms forming an almost flat construct. tested with peptide bonds, phenyls, histidines. an optional tolerance keyword allows to specify the maximum difference from a flat structure. default is 5 degrees.
- determination of atom properties based on other information (e.g. element from mass, mass from element, element from name, radius from element).
- support for reading and writing of xmol/xyz style trajectories with a varying number of atoms
- support for writing (fake!) gromacs topology files for use with gromacs analysis tools for non-gromacs trajectories.
- support for reading data files containing non-orthogonal cells.
- stricter checking for CGCMM extensions to the data file format. only if the string CGCMM is in the first line of the data file, the lammps data file parser will look for those extensions.
- encode the intended atom_style setting in data file header. Parse and compare - if present - against requested atom style on reading.
- write commented out Coeff sections to data files to provide hints on which coefficients need to be set.

Version 1.2

The final version of TopoTools-v1.2 has been released with VMD version 1.9.1.

This version contains important bugfixes in topo guessatom (one of which affects topo readvarxyz), a few small enhancements, and a much improved and expanded documentation in addition to the tutorial on this homepage.

New features:
- 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)
- Bugfixes in 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 1.3

The final version of TopoTools-v1.3 scheduled to be released with 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
- Better detection of unknown topo subcommands
- Better detection for insufficient data when parsing the Atoms section in LAMMPS data files

Installation

unpack the tar archive which will create a directory named topotools1.2, and move it next to the topotools1.1 directory from your existing VMD 1.9 installation. VMD should use the new version automatically at the next start. To uninstall, just remove the topotools1.2 directory.
Č
ċ
ď
v.1
topotools-1.2-20120114.tar.gz
(39k)
Axel Kohlmeyer,
Jan 14, 2012 6:28 PM
ċ
ď
v.2
topotools-1.3-20120215.tar.gz
(39k)
Axel Kohlmeyer,
Feb 15, 2012 6:00 PM
Ċ
ď
v.1
topotools-slides.pdf
(112k)
Axel Kohlmeyer,
Mar 2, 2010 3:02 PM