complex_bilayer_builder_driver.py Command Help
Command: $SCHRODINGER/run complex_bilayer_builder_gui_dir/complex_bilayer_builder_driver.py
usage: $SCHRODINGER/run complex_bilayer_builder_gui_dir/complex_bilayer_builder_driver.py
[-h] -upper_leaflet_comp UPPER_LEAFLET_COMP UPPER_LEAFLET_COMP
-lower_leaflet_comp LOWER_LEAFLET_COMP LOWER_LEAFLET_COMP -box_xy
BOX_XY BOX_XY -water_padding WATER_PADDING
[-custom_lipid_files CUSTOM_LIPID_FILES [CUSTOM_LIPID_FILES ...]]
[-custom_lipid_smiles CUSTOM_LIPID_SMILES [CUSTOM_LIPID_SMILES ...]]
[-protein_structure PROTEIN_STRUCTURE] [-membrane_channel]
[-solvent {SPC,SPCE,TIP3P,TIP4P,TIP4P2005,TIP4PEW,TIP4PD,TIP5P,none}]
[-salt SALT SALT] [-neutralize]
[-salt_concentration SALT_CONCENTRATION]
[-custom_lipid_names CUSTOM_LIPID_NAMES [CUSTOM_LIPID_NAMES ...]]
[-double_bond_stereochem {True,False,UNDEFINED,None} [{True,False,UNDEFINED,None} ...]]
[-chiral_center_stereochem {True,False,UNDEFINED,None} [{True,False,UNDEFINED,None} ...]]
[-include_nonphospholipids {True,False,UNDEFINED} [{True,False,UNDEFINED} ...]]
[-custom_msj CUSTOM_MSJ] [-forcefield FORCEFIELD] [-md_umbrella]
[-seed SEED] [-OPLSDIR OPLSDIR]
options:
-h, -help Show this help message and exit.
-upper_leaflet_comp UPPER_LEAFLET_COMP UPPER_LEAFLET_COMP
Lipid composition of the upper leaflet, including
lipid types and ratio of each type, in the format of
lipid1:lipid2 ratio1:ratio2. For example, POPC:POPE
2:1 means for every 2 POPC molecules, there should be
1 POPE molecule. If providing a custom lipid
(-custom_lipid_files or -custom_lipid_smiles), use the
custom lipid name here as it appears in an argument of
-custom_lipid_names. (default: None)
-lower_leaflet_comp LOWER_LEAFLET_COMP LOWER_LEAFLET_COMP
Lipid composition of the lower leaflet, including
lipid types and ratio of each type, in the format of
lipid1:lipid2 ratio1:ratio2. For example, POPC:POPE
2:1 means for every 2 POPC molecules, there should be
1 POPE molecule. If providing a custom lipid
(-custom_lipid_files or -custom_lipid_smiles), use the
custom lipid name here as it appears in an argument of
-custom_lipid_names. (default: None)
-box_xy BOX_XY BOX_XY
Length of the box in x and y dimensions. For example,
50 50 (default: None)
-water_padding WATER_PADDING
Water padding or height of water above and below the
membrane. (default: None)
-custom_lipid_files CUSTOM_LIPID_FILES [CUSTOM_LIPID_FILES ...]
Custom lipid (structure file), if not available in the
library. If used with -custom_lipid_smiles, use "None"
as the argument here when a SMILES string is defined.
The library currently includes CHL, DMPC, DPPC, POPC,
POPE lipids. (default: None)
-custom_lipid_smiles CUSTOM_LIPID_SMILES [CUSTOM_LIPID_SMILES ...]
Custom lipid (SMILES string), if not available in the
library. If used with -custom_lipid_files, use "None"
as the argument here when a structure file is defined.
The library currently includes CHL, DMPC, DPPC, POPC,
POPE lipids. (default: None)
-protein_structure PROTEIN_STRUCTURE
Protein structure if any. If not provided, the system
will be pure lipid bilayer. (default: None)
-membrane_channel Use if the provided protein structure has a channel
that needs to be hydrated. (default: False)
-solvent {SPC,SPCE,TIP3P,TIP4P,TIP4P2005,TIP4PEW,TIP4PD,TIP5P,none}
Type of water used for hydrating the system. (default:
SPC)
-salt SALT SALT Salt or other charged molecules. Requires 2 inputs, a
cation and an anion, in that order. For each input,
there are two options: (1) Choose from the available
cation and anions (case sensitive). Available ions:
Li+, Na+, K+, Rb+, Cs+, Mg2+, Ca2+, Zn2+, Fe2+, Fe3+,
F-, Cl-, Br-, I-. (2) Add a structure file. (default:
['Na+', 'Cl-'])
-neutralize Neutralize the system. (default: False)
-salt_concentration SALT_CONCENTRATION
Concentration of the salt in Molar (M) to add to the
system. (default: None)
-custom_lipid_names CUSTOM_LIPID_NAMES [CUSTOM_LIPID_NAMES ...]
Custom lipid names. Cannot be more than 4-characters.
Each custom lipid must have a name. (default: None)
-double_bond_stereochem {True,False,UNDEFINED,None} [{True,False,UNDEFINED,None} ...]
If True, use cis double bond stereochemistry for the
custom lipid; if False, use trans double bond
stereochemistry; if None, do not set the double bond
stereochemistry. Each custom lipid must have a
True/False/None value. If this flag is not used, it
will default to True (cis stereochemistry) for each
custom lipid. (default: UNDEFINED)
-chiral_center_stereochem {True,False,UNDEFINED,None} [{True,False,UNDEFINED,None} ...]
If True, make all chiral centers R-chiral for the
custom lipid; if False, make all chiral centers
S-chiral; if None, do not set the chirality of chiral
centers. Each custom lipid must have a True/False/None
value. If this flag is not used, it will default to
None for each custom lipid. (default: UNDEFINED)
-include_nonphospholipids {True,False,UNDEFINED} [{True,False,UNDEFINED} ...]
If True, include the custom lipid even if it is not a
phospholipid. Each custom lipid must have a True/False
value. If this flag is not used, it will default to
True for each custom lipid. (default: UNDEFINED)
-custom_msj CUSTOM_MSJ
Provide a custom msj file to be used in case the
built-in relaxation protocol fails or to be used as a
continuation of the built-in relaxation protocol.
(default: None)
-forcefield FORCEFIELD
Specify the force field to use. (default: S-OPLS)
-md_umbrella Run desmond subjobs on the driver host. (default:
False)
-seed SEED Seed for random number generator. (default: 1234)
Job Control Options:
-OPLSDIR OPLSDIR Specifies directory for custom forcefield parameters.
(default: None)