期刊
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
卷 25, 期 2, 页码 247-260出版社
ELSEVIER SCIENCE INC
DOI: 10.1016/j.jmgm.2005.12.005
关键词
atom type perception; bond type perception; antechamber; residue topology; force field parameters; general AMBER force field (GAFF)
类别
资金
- NIGMS NIH HHS [GM-56531] Funding Source: Medline
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. (c) 2005 Elsevier Inc. All rights reserved.
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