TY - JOUR
T1 - Automatic atom type and bond type perception in molecular mechanical calculations
AU - Wang, Junmei
AU - Wang, Wei
AU - Kollman, Peter A.
AU - Case, David A.
N1 - Funding Information:
This paper is dedicated to Peter A. Kollman, who initiated and directed this work prior to his death in May 2001. J.M.W. is grateful to acknowledge computer time at NCSA (MCB000013N (J. Wang, P. I.)). D.A.C. was supported by NIH grant GM-56531. The Antechamber program, which is licensed under GNU General Public Library, is available at http://amber.scripps.edu/antechamber/antechamber.html .
PY - 2006/10
Y1 - 2006/10
N2 - 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.
AB - 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.
KW - Antechamber
KW - Atom type perception
KW - Bond type perception
KW - Force field parameters
KW - General AMBER force field (GAFF)
KW - Residue topology
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U2 - 10.1016/j.jmgm.2005.12.005
DO - 10.1016/j.jmgm.2005.12.005
M3 - Article
C2 - 16458552
AN - SCOPUS:33748538349
VL - 25
SP - 247
EP - 260
JO - Journal of Molecular Graphics and Modelling
JF - Journal of Molecular Graphics and Modelling
SN - 1093-3263
IS - 2
ER -