molcharge Appendix: Complete list of -method optionsΒΆ

While there are many allowed options for the -method parameter in molcharge, only am1bccsym, mmff (Default), amberff99sb, and gasteiger are recommended (indicated in italics). The full list is given below:

am1 applies the AM1 semiempirical method to derive the atomic charges for the molecule. A full geometry optimization is carried out. A 3D geometry for the input molecule is required.

am1spt applies the AM1 semiempirical method to derive the atomic charges for the molecule. Only a single-point calculation is carried out, so it is much faster but also very sensitive to the input geometry (bad charges from a bad geometry). A 3D geometry for the input molecule is required.

am1bcc is a synonym for am1bccnosym (described below).

Note

Note that this differs from the “standard” AM1BCC charging scheme as published, where symmetrization is done (same as am1bccsym).

am1bccnosym applies AM1BCC charges, but without averaging bond-topologically symmetric charges. The partial semiempirical AM1 geometry optimization is done. It requires a 3D geometry associated with an input structure. Non-symmetric charges can lead to problems with geometry optimizations and with multi-conformer molecules.

am1bccsym (recommended) applies AM1BCC charges as published, including partial semiempirical AM1 geometry optimization and averaging bond-topologically symmetric charges. It requires a 3D geometry associated with an input structure. These are good- quality charges for intermolecular interactions involving organic molecules.

am1bccspt is a synonym for am1bccnosymspt (described below).

am1bccnosymspt applies AM1BCC charges as published, but without averaging bond-topologically symmetric charges. Only a single-point AM1 calculation is carried out, so it is much faster but also very sensitive to the input geometry (bad charges from a bad geometry). A 3D geometry for the input molecule is required.

am1bccsymspt applies AM1BCC charges as published, averaging bond-topologically symmetric charges. Only a single-point AM1 calculation is carried out, so it is much faster but also very sensitive to the input geometry (bad charges from a bad geometry). A 3D geometry for the input molecule is required.

amberff99sb (recommended) applies to proteins the RESP charge set used for Amber forcefields ff94, ff96, ff98, ff99, ff99sb, and ff99sbc0 (the same charge set is used in all these cases). This method only works for standard amino acids. These are very good-quality charges for intermolecular interactions involving proteins.

am1bccelf10 charging is designed to average the AM1BCC charges from 10 conformers chosen from the 2% of the conformer population having the Electrostatically Least-interacting Functional (ELF) groups. 10 conformers from 2% means there must be at least 500 conformers to start with; ligands which have fewer rotatable bonds may not have this many. In such cases, this method is designed to take all the conformers in the 2% ELF population.

amberff94, amberff99, and amberff99bsc0 are synonyms for amberff99sb The Amber forcefields use the same RESP charge set all cases

gasteiger (recommended) applies Gasteiger charges (a charge-equilibration method).

Note

This method should not be used for intermolecular interactions. This method was intended for comparing relative reactivity of related organic chemical functional groups within different molecular contexts. It will work with only a 2D geometry.

mmff (recommended) applies MMFF94 charges. It only requires a 2D geometry. This method ia the best choice for use with the MMFF forcefield and these charges are of passable quality for intermolecular interactions. This is the default method.

initial sets the charges to the MMFF94 initial fractional charges used for charged functional groups, smearing unit charges in the partial charge field onto resonance shared atoms.

formal copies the formal charge field of atoms into the partial charge field.

none sets the partial charges to zero.