*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:

am1applies 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.

am1sptapplies 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.

am1bccis a synonym foram1bccnosym(described below).Note

Note that this differs from the “standard”

AM1BCCcharging scheme as published, where symmetrization is done (same asam1bccsym).

am1bccnosymapplies AM1BCC charges, butwithoutaveraging 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.

am1bccsptis a synonym foram1bccnosymspt(described below).

am1bccnosymsptapplies AM1BCC charges as published, butwithoutaveraging 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.

am1bccsymsptapplies 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.

am1bccelf10charging 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, andamberff99bsc0are synonyms foramberff99sbThe 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.

initialsets 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.

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

nonesets the partial charges to zero.