autosolvate.solventBoxBuilder

class autosolvate.solventBoxBuilder(xyzfile, solvent='water', slu_netcharge=0, cube_size=54, charge_method='resp', slu_spinmult=1, outputFile='', srun_use=False, qm_program='gaussian', qm_exe=None, qm_dir=None, amberhome=None, closeness=0.8, solvent_off='', solvent_frcmod='', rundir='')[source]

Solvated molecule in specified solvent.

Parameters:

  • solvent (str, Optional, default: ‘water’) – Currently implemented solvents are: ‘water’, ‘methanol’, ‘chloroform’, ‘nma’, ‘acetonitrile’

  • slu_netcharge (int, Optional, default 0) – Charge of solute, the solvent box will be neutralized with Cl- and Na+ ions

  • cube_size (float, Optional, default: 54) – Size of MM solvent box

  • charge_method (str, Optional, default: “resp”) – Use ‘resp’ (quantum mechanical calculation needed) or ‘bcc’ to estimate partial charges

  • slu_spinmult (int, Optional, default: 1) – Spinmultiplicity of solute

  • outputFile (str, Optional, default=’water_solvated’) – Filename-prefix for outputfiles

  • srun_use (bool, Optional, default=’False) – Run all commands with a srun prefix

Returns:

To run solvation, call build function.

Return type:

None

__init__(xyzfile, solvent='water', slu_netcharge=0, cube_size=54, charge_method='resp', slu_spinmult=1, outputFile='', srun_use=False, qm_program='gaussian', qm_exe=None, qm_dir=None, amberhome=None, closeness=0.8, solvent_off='', solvent_frcmod='', rundir='')[source]

Methods

__init__(xyzfile[, solvent, slu_netcharge, ...])

build()

Run solventBoxBuilder

createAmberParm()

Generate Amber parameters with tleap

createLib()

Run tleap

getFrcmod()

Get partial charges and create frcmod

getHeadTail()

Detect start and end of coordinates

getSolutePDB()

Convert xyz to pdb

inputCheck()

packSLUSLV()

Write packmol input file for custom solvents

processPackmolPDB()

Convert file for custom solvents like CH3CN

removeConectFromPDB()

writeTleapcmd1()

Create tleap input file

writeTleapcmd_add_solvent()

Write tleap input file to add solvent

writeTleapcmd_add_solvent_custom()

Write tleap input file to add solvent from user provided .off and .frcmod files

writeTleapcmd_custom_solvated()

Write tleap file for custom solvents like CH3CN