autosolvate.startboxgen
- autosolvate.startboxgen(argumentList)[source]
Wrap function that parses command line options for autosolvate boxgen, adds solvent box to a given solute, and generates related force field parameters.
- 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
- Returns
Generates the structure files and save as
`.pdb`. Generates the MD parameter-topology and coordinates files and saves as`.prmtop`and`.inpcrd`- Return type
None