Automatic atom type and bond type perception in molecular mechanical calculations

Junmei Wang, Wei Wang, Peter A. Kollman, David A. Case

Research output: Contribution to journalArticle

2209 Scopus citations

Abstract

In molecular mechanics (MM) studies, atom types and/or bond types of molecules are needed to determine prior to energy calculations. We present here an automatic algorithm of perceiving atom types that are defined in a description table, and an automatic algorithm of assigning bond types just based on atomic connectivity. The algorithms have been implemented in a new module of the AMBER packages. This auxiliary module, antechamber (roughly meaning "before AMBER"), can be applied to generate necessary inputs of leap-the AMBER program to generate topologies for minimization, molecular dynamics, etc., for most organic molecules. The algorithms behind the manipulations may be useful for other molecular mechanical packages as well as applications that need to designate atom types and bond types.

Original languageEnglish (US)
Pages (from-to)247-260
Number of pages14
JournalJournal of Molecular Graphics and Modelling
Volume25
Issue number2
DOIs
StatePublished - Oct 1 2006

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Keywords

  • Antechamber
  • Atom type perception
  • Bond type perception
  • Force field parameters
  • General AMBER force field (GAFF)
  • Residue topology

ASJC Scopus subject areas

  • Spectroscopy
  • Physical and Theoretical Chemistry
  • Computer Graphics and Computer-Aided Design
  • Materials Chemistry

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