determination of atom properties based on other information (e.g. an optional tolerance keyword allows to specify the maximum difference from a flat structure. tested with peptide bonds, phenyls, histidines. searches for atoms bound to exactly three other atoms forming an almost flat construct. determination of angle and dihedral definitions from bonding information. Several bugfixes, especially for operating on selections and assigning atom properties. 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).
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.
Modelling Enzymatic Mechanisms with QM/MM Approaches: Current Status and Future Challenges.TopoTools is a VMD plugin for manipulating topology information. The complete catalytic mechanism of xanthine oxidase: a computational study. An Unsual Cys‐Glu‐Lys Catalytic Triad is Responsible for the Catalytic Mechanism of the Nitrilase Superfamily: A QM/MM Study on Nit2. Molecular dynamics: a powerful tool for studying the medicinal chemistry of ion channel modulators. Discovery of TGFBR1 (ALK5) as a potential drug target of quercetin glycoside derivatives (QGDs) by reverse molecular docking and molecular dynamics simulation.
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