ProtoCaller.Solvate package

This package handles solvation of systems. So far, it only contains one general function, solvate(), which should be able to deal with most solvation scenarios. Keep in mind that this package depends on a GROMACS binary being installed on your system and it being accessible either via terminal or through a GROMACSHOME environment variable.

Module contents

ProtoCaller.Solvate.solvate(complex, params=None, box_length=8, shell=0, neutralise=True, ion_conc=0.154, centre=True, work_dir=None, filebase='complex')

Uses gmx solvate and gmx genion to solvate the system and (optionally) add NaCl ions. This function preserves the crystal water molecules.

Parameters

  • complex (BioSimSpace.System or parmed.structure.Structure) – The input unsolvated system.

  • params (ProtoCaller.Parametrise.Params) – The input force field parameters.

  • box_length (float, iterable) – Size of the box in nm.

  • shell (float) – Places a layer of water of the specified thickness in nm around the solute.

  • neutralise (bool) – Whether to add counterions to neutralise the system.

  • ion_conc (float) – Ion concentration of NaCl in mol/L.

  • centre (bool) – Whether to centre the system.

  • work_dir (str) – Work directory. Default: current directory.

  • filebase (str) – Output base name of the file.

Returns

complex – The solvated system.

Return type

BioSimSpace.System or parmed.structure.Structure