schrodinger.application.desmond.mxmd.mxmd_system_builder module

Script to setup cosolvent system

class schrodinger.application.desmond.mxmd.mxmd_system_builder.Cosolvent(pdbtype, density, mass, nheavy, filename)

Bases: tuple

density

Alias for field number 1

filename

Alias for field number 4

mass

Alias for field number 2

nheavy

Alias for field number 3

pdbtype

Alias for field number 0

schrodinger.application.desmond.mxmd.mxmd_system_builder.convert_vv2mol(probe_name: str, target_vv_ratio: float = 5.0) → int

This function reports the number of water molecules required to maintain the required volume/volume ratio for each molecules of the probe Assumes that density is provided in gm/cm3 molecular mass also should be specified in gm/mol :param probe_name: Name of the cosolvent used to build mixed-solvent box :param target_vv_ratio: Volume over volume ratio in percent

class schrodinger.application.desmond.mxmd.mxmd_system_builder.CosolventBoxGenerator(solute_fname: str, probe_name: str, box_number: int, init_water_buffer: float = 12.0, cosolvent_layer_size: float = 7.0, cosolvent_volume_ratio: float = 5.0, cosolvent_vdw_scaling: Union[float, NoneType] = None, water='SPC')

Bases: object

Example:

gen = CosolventBoxGenerator(

inp_fname, ‘acetonitrile’, 1, cosolvent_layer_size=5.0, cosolvent_volume_ratio=2.0)

gen.generate(out_fname)

generate(fname: str) → None