autosolvate.multicomponent.startmulticomponent

autosolvate.multicomponent.startmulticomponent(args)

Wrap function that parses command line options for autosolvate multicomponent module, generate solvent box and related force field parameters. suggested usage: autosolvate multicomponent -f <JSON path>

Command Line Options

-f, --file

json file containing the input parameters, Required when using multiple solvents. Will ignore all other options if provided.

-m, --main

solute xyz file, An Legacy feature, designed for the compatibility with the older version. It is not recommended for further use.

-o, --output

prefix of the output file names

-c, --charge

formal charge of solute

-u, --spinmultiplicity

spin multiplicity of solute

-s, --solvent

solvent xyz files, Will use single solvent if provided. Not available for using multiple solvents

-g, --chargemethod

name of charge fitting method (bcc, resp)

-b, --cubesize

size of solvent cube in angstroms

-t, --closeness

Solute-solvent closeness setting. Default 2.0 Å for mixed solvent. For acetonitrile tolerance parameter in packmol in Å, for water, methanol, nma, chloroform the scaling factor in tleap, setting to ‘automated’ will automatically set this parameter based on solvent.

-r, --srunuse

option to run inside a slurm job

-e, --gaussianexe

name of the Gaussian quantum chemistry package executable used to generate electrostatic potential needed for RESP charge fitting

-d, --gaussiandir

path to the Gaussian package

-a, --amberhome

path to the AMBER molecular dynamics package root directory. Definition of the environment variable $AMBERHOME

-h, --help

short usage description

rtype:

Generates the structure files and save as `.pdb`. Generates the MD parameter-topology and coordinates files and saves as `.prmtop` and `.inpcrd`