Automatic atom type and bond type perception in molecular mechanical calculations. Export

@article{citeulike:3740748, 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.}, address = {College of Chemistry, Peking University, Beijing 100871, China.}, author = {Wang, Junmei and Wang, Wei and Kollman, Peter A. A. and Case, David A. A.}, citeulike-article-id = {3740748}, citeulike-linkout-0 = {http://dx.doi.org/http://dx.doi.org/10.1016/j.jmgm.2005.12.005}, citeulike-linkout-1 = {http://dx.doi.org/10.1016/j.jmgm.2005.12.005}, doi = {http://dx.doi.org/10.1016/j.jmgm.2005.12.005}, journal = {J Mol Graph Model}, keywords = {ab-initio, antechamber, coletta, parametrization}, month = {February}, posted-at = {2008-12-03 15:12:09}, priority = {2}, title = {Automatic atom type and bond type perception in molecular mechanical calculations.}, url = {http://dx.doi.org/http://dx.doi.org/10.1016/j.jmgm.2005.12.005}, year = {2006} }

TY - JOUR ID - citeulike:3740748 L3 - citeulike-article-id:3740748 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. JF - J Mol Graph Model AD - College of Chemistry, Peking University, Beijing 100871, China. TI - Automatic atom type and bond type perception in molecular mechanical calculations. KW - ab-initio KW - antechamber KW - coletta KW - parametrization AU - Wang, Junmei AU - Wang, Wei AU - Kollman, Peter AU - Case, David PY - 2006/February// UR - http://dx.doi.org/http://dx.doi.org/10.1016/j.jmgm.2005.12.005 ER -