Options of mk_prepare_receptor.py

Contents

Options of mk_prepare_receptor.py#

Input/Output Options#

--read_pdb <PDB_FILENAME>#: Read a PDB file using the PDB parser in RDKit.

-i, --read_with_prody <MACROMOL_FILENAME>#: Read a PDB or mmCIF file using ProDy (if installed). ProDy can be installed from PyPI or conda-forge.

-o, --output_basename <basename>#: Specify a default basename for output files created by –write options when no filename is specified.

-p, --write_pdbqt <PDBQT_FILENAME> [*]#: Output PDBQT files with _rigid or _flex suffixes for flexible residues. Defaults to –output_basename if no filename is provided.

-j, --write_json <JSON_FILENAME> [*]#: Save the receptor’s parameterized configuration to JSON format. Defaults to –output_basename if unspecified.

-g, --write_gpf <GPF_FILENAME> [*]#: Output an AutoGrid input file (GPF). Defaults to –output_basename if not specified.

-v, --write_vina_box <VINA_BOX_FILENAME> [*]#: Generate a configuration file for Vina with grid box dimensions. Defaults to –output_basename if not specified.

--write_pdb <PDB_FILENAME> [*]#: Save the prepared receptor in PDB format. Must specify the filename.

Receptor Perception Options#

-n, --set_template <template>#: Assign templates to residues, e.g., A:5,7=CYX,B:17=HID.

-d, --delete_residues <residues>#: Specify residues to delete, e.g., A:350,B:15,16,17.

-b, --blunt_ends <positions>#: Blunt end definitions, e.g., A:123,200=2,A:1=0.

--add_templates <JSON_FILENAME> [*]#: Load additional templates from one or more JSON files.

-a, --allow_bad_res#: (Flag) Ignore residues with missing atoms instead of raising an error.

--default_altloc <location>#: Define a default alternate location for residues, overridden by –wanted_altloc.

--wanted_altloc <location>#: Specify alternate locations for particular residues, e.g., :5=B,B:17=A.

--mk_config <JSON_FILENAME>#: Specify a JSON configuration file for receptor preparation.

Grid Box Options#

--box_size <X Y Z>#: Set the size of the grid box in Angstroms (x, y, z).

--box_center <X Y Z>#: Define the center of the grid box in Angstroms (x, y, z).

--box_center_off_reactive_res#: (Flag) Shift the grid box center 5 Å along the CA-CB bond from CB. Applicable only when there is one reactive flexible residue.

--box_enveloping <FILENAME>#: Adjust the grid box to enclose atoms in the specified file. Supported formats: .sdf, .mol, .mol2, .pdb, .pdbqt.

--padding <value>#: Set padding around atoms specified in –box_enveloping (in Å).

Flexible and/or Reactive Options#

-f, --flexres <residues>#: Define flexible residues by chain ID and residue number, e.g., -f “:42,B:23”.

-r, --reactive_flexres <residues>#: Define reactive flexible residues by chain ID and residue number, e.g., -r “:42,B:23”. Maximum of 8 reactive residues.

--reactive_name <residue:atom>#: Specify the reactive atom name for a residue type, e.g., –reactive_name “TRP:NE1”. Can be repeated for multiple assignments.

-s, --reactive_name_specific <residue:atom>#: Specify the reactive atom for an individual residue by residue ID, e.g., -s “A:42=NE2”. The residue becomes reactive.

--r_eq_12 <value>#: Set the equilibrium distance (r_eq) for reactive atoms in 1-2 interactions. Default is 1.8 Å.

--eps_12 <value>#: Set the epsilon value for reactive atoms in 1-2 interactions. Default is 2.5.

--r_eq_13_scaling <factor>#: Scale r_eq for 1-3 interactions across reactive atoms. Default is 0.5.

--r_eq_14_scaling <factor>#: Scale r_eq for 1-4 interactions across reactive atoms. Default is 0.5.