Antechamber, An Accessory Software Package For Molecular Mechanical Calculations

  • Wang J
  • Wang W
  • Kollman P
 et al. 
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We present a set of auxiliary programs for molecular mechanics studies on a wide class of organic molecules. This software package is devoted to solve the following problems: (1) identifying bond and atom types; (2) judging atomic equivalence; (3) generating residue topology files; and (4) finding missing force field parameters and supplying reasonable suggestions. As an accessory module in the AMBER 7 and AMBER 8 packages, antechamber can generate input automatically for most organic molecules in a database. The algorithms behind these manipulations are presented here, and may be useful outside the Amber family of programs as well.

Author-supplied keywords

  • antechamber
  • atom type recognition
  • bond type recognition
  • field parameters
  • force
  • gaff
  • general amber force field
  • residue topology

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  • Junmei Wang

  • Wei Wang

  • Peter a Kollman

  • David a Case

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