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