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B.1 Development of the PARAM1 Parameter Set

by David J. States

This essay describes the PARAM1 parameterization for the CHARMM molecular modelling program, compiled in May of 1981 by David States. My goal was to obtain a documented set of parameters which described the experimentally observable properties of small molecules as well as possible in the context of the CHARMM potential energy form. This was achieved by a combination of explicit least squares fitting where possible, and trial and error model building where it was not. Extended atom representations were used for aliphatic and aromatic hydrogens with the exception of benzene, where it was necessary to model the system using both extended and all hydrogen potentials. Explicit hydrogens were used for all protonated heteroatoms. Parameters have been included in the parameter file for atom types used in the PROT and ALLH topology files by generalizing the most appropriate HPRO parameter (ex. using the C-NH1 bond constants for C-NH1E).