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# molcharge Usage¶

molcharge uses the -method flag to determine what method to use to generate partial charges. Some methods can be applied to 2D input structures, others require 3D input structures; for the latter the run will fail if a 3D structure is not provided. Hydrogens will be sprouted on the molecules if they are not present already.

With default parameters, molcharge will sprout explicit hydrogens and assign MMFF94 partial charges.

## Required Parameters¶

-in

This is the input file. This file can contain molecules in a wide-variety of molecular formats. Some of the partial charging models, such as AM1 and AM1BCC require coordinates in order to calculate charges. While the input file is required, the -in flag is optional. If no -in flag is specified, the first unflagged parameter is used as the input file.

-out

This is the output file and it is a required parameter. Since the object of molcharge is to generate partial charges, it will only write to formats that can specify a partial charge. These formats currently include only .mol2, .mol2H and .oeb. While the output file is required, the -out flag is optional. If no -out flag is specified, the second unflagged parameter is used as the output file.

### Optional parameters¶

-method {option}

Selects the charging method to be applied to the input molecule(s). Choose one of the following recommended options:

am1bccsym 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 pharmaceutical organic molecules for intermolecular interactions.

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

amberff99sb 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 proteins for intermolecular interactions.

gasteiger 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.

There are a number of other options for charge methods, but none are recommended. They are listed in the molcharge appendix.

-param

The argument for this flag is the name of a file containing control parameters. The control parameter file acts to either replace or augment the command line interface. All parameters necessary for program execution may be provided in the control parameter file, although any command given explicitly on the command line will supersede options found in the parameter file. molcharge generates a new parameter file containing the full set of execution parameters upon every execution. The name of the parameter file written by molcharge is created by combining the prefix base name with the ‘.parm’ extension.

-paramfile

The filename for the output parameter file can be set with this flag and it overrides -prefix flag for the name of parameter file.

-prefix

The argument for this flag defines the prefix to be used for parameter and log files. The parameter and log files will be written to what follows this flag plus the extension .param or .log. [default = molcharge]

## Example Commands¶

An example run of the molcharge program is given below.

prompt> molcharge -method mmff drugs.sdf drugs.mol2


This executes molcharge with the default parameters, to sprout explicit hydrogens and assign MMFF94 partial charges. The file drugs.sdf is opened in SD format for input, and the output is written to the file drugs.mol2 in Sybyl .mol2 format.

prompt> molcharge -method amberff99sb 2iko_prot.pdb 2iko_prot.oeb


In this sample execution, a protein is charged using the Amber charge set and written to OEB format.

# molcharge Appendix: Complete list of -method options¶

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.