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Development of an internal searching algorithm for parameterization of the MM2/MM3 force fields
Author(s) -
Schnur Dora M.,
Grieshaber Mark V.,
Bowen J. Phillip
Publication year - 1991
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.540120709
Subject(s) - force field (fiction) , set (abstract data type) , algorithm , field (mathematics) , computer science , process (computing) , order (exchange) , analogy , mathematics , artificial intelligence , pure mathematics , finance , economics , programming language , operating system , linguistics , philosophy
Application of Allinger's MM2/MM3 force fields to molecules of real interest is frequently hindered by the lack of parameters for various heterocyclic systems and for poly‐functionalized molecules. A common approach to this problem is to manually choose missing parameters “by analogy” with those that are part of the force field's internal parameter set. Naturally, this is generally attempted only by those possessing extensive experience with force fields. In order to use the MM2/MM3 force fields to study herbicides, an algorithm has been developed to automate this process for the non MM2 specialist. Using a set of “relative cost” criteria for atom type replacement, the algorithm searches the force field parameter set and selects the most appropriate parameters for a given molecule whose MM2 output file contains “missing parameter” errors. The program selects parameter error messages from a standard MM2 output file, finds analogous parameters, asks the user to verify their appropriateness and creates a standard MM2 parameter deck for the molecule of interest.