Wrap function that parses command line options for autosolvate boxgen, adds solvent box to a given solute, and generates related force field parameters.


argumentList (list) – The list contains the command line options to specify solute, solvent, and other options related to structure and force field parameter generation.

Command line option definitions
-m, --main

solute xyz file

-s, --solvent

name of solvent (water, methanol, chloroform, nma)

-o, --output

prefix of the output file names

-c, --charge

formal charge of solute

-u, --spinmultiplicity

spin multiplicity of solute

-g, --chargemethod

name of charge fitting method (bcc, resp)

-b, --cubesize

size of solvent cube in angstroms

-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

-t, --closeness

Solute-solvent closeness setting, 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.

-l, --solventoff

path to the custom solvent .off library file. Required if the user want to use some custom solvent other than the 5 solvents contained in AutoSolvate (TIP3P water, methanol, NMA, chloroform, MeCN)

-p, --solventfrcmod

path to the custom solvent .frcmod file. Required if the user wants to use some custom solvent other than the 5 solvents contained in AutoSolvate.

-h, --help

short usage description


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

Return type