Program Options

The arguments and inputs of the various QMrebind programs are described here.

run_qmrebind_amber.py

Run run_qmrebind_amber.py with the ‘-h’ argument to see all available arguments:

python run_qmrebind_amber.py -h

usage:

python run_qmrebind_amber.py [-h] [-l LIGAND_INDICES] [-L LIGAND_RESNAME]
                           [-o OUTPUT] [-c CUT_OFF_DISTANCE] [-n NPROCS]
                           [-i MAX_ITERATIONS] [-m QM_METHOD]
                           [-b QM_BASIS_SET] [-s QM_CHARGE_SCHEME]
                           [-q QM_CHARGE] [-u QM_MULTIPLICITY]
                           [-M QM2_METHOD] [-S QM2_CHARGE_SCHEME]
                           [-Q QM2_CHARGE] [-U QM2_MULTIPLICITY]
                           [-O ORCA_PATH] [-w WORK_DIR] [-x]
                           INPUT_PDB FORCEFIELD_FILE

Required Arguments

INPUT_PDB: The name of a PDB file of a molecular system. The PDB should contain box information in a CRYST line, and have receptor atoms, ligand atoms, and solvent atoms included as contiguous lines, in that order.
FORCEFIELD_FILE: The name of a AMBER input .parm7 (or .prmtop) file, which contains existing system FF parameters, some of which will by overwritten (typically the partial charges of the ligand).

Optional Arguments

-h, --help

show help message and exit

-l LIGAND_INDICES, --ligand_indices LIGAND_INDICES

A comma-separated list of integers defining site within the ref_pdb structure. Ex: -l ‘1,2,0’. Either the ‘-l’ or ‘-L’ arguments must be included.

-L LIGAND_RESNAME, --ligand_resname LIGAND_RESNAME

The residue name of the ligand molecule for automatic index selection. Either the ‘-l’ or ‘-L’ arguments must be included.

-o OUTPUT, --output OUTPUT

A path to an output file name for the forcefield file. If left at the default of None, a file will be generated in the work directory with the same name as the input forcefield file. Default: None.

-c CUT_OFF_DISTANCE, --cut_off_distance CUT_OFF_DISTANCE

The cut-off distance (in Angstroms) used to define the QM2 region of the ONIOM calculation. Default: 3.0.

-n NPROCS, --nprocs NPROCS

The number of processors to use for ORCA calculations. Default: 1.

-i MAX_ITERATIONS, --max_iterations MAX_ITERATIONS

The maximum number of iterations for ORCA convergence. Default: 2000.

-m QM_METHOD, --qm_method QM_METHOD

The method to use for the QM region of the ONIOM calculation. Please see the file orca_methods_basis_sets.pdf for all possible options. Default: B3LYP.

-b QM_BASIS_SET, --qm_basis_set QM_BASIS_SET

The basis set to use for the QM region of the ONIOM calculation. Please see the file orca_methods_basis_sets.pdf for all possible options. Default: 6-311G.

-s QM_CHARGE_SCHEME, --qm_charge_scheme QM_CHARGE_SCHEME

The charge scheme to use for the QM region of the ONIOM calculation. Please see the file orca_methods_basis_sets.pdf for all possible options. Default: CHELPG.

-q QM_CHARGE, --qm_charge QM_CHARGE

The total charge of the QM region of the ONIOM calculation. Default: 0.

-u QM_MULTIPLICITY, --qm_multiplicity QM_MULTIPLICITY

The multiplicity of the QM region of the ONIOM calculation. Default: 1.

-M QM2_METHOD, --qm2_method QM2_METHOD

The method to use for the QM2 region of the ONIOM calculation. Please see the file orca_methods_basis_sets.pdf for all possible options. Default: XTB.

-S QM2_CHARGE_SCHEME, --qm2_charge_scheme QM2_CHARGE_SCHEME

The charge scheme to use for the QM2 region of the ONIOM calculation. Please see the file orca_methods_basis_sets.pdf for all possible options. Default: CHELPG.

-Q QM2_CHARGE, --qm2_charge QM2_CHARGE

The total charge of the QM2 region of the ONIOM calculation. Default: 0.

-U QM2_MULTIPLICITY, --qm2_multiplicity QM2_MULTIPLICITY

The multiplicity of the QM2 region of the ONIOM calculation. Default: 1.

-O ORCA_PATH, --orca_path ORCA_PATH

An absolute path to the ORCA program. If not specified, ORCA will be found from the shutil.which() command. Default: None.

-w WORK_DIR, --work_dir WORK_DIR

A working directory for all temporary files, log files, etc. If left at None, a work directory will be automatically generated in the current directory. Default: None.

-x, --skip_checks

By default, checks will be run at various stages of Qmrebind, and if the checks fail, the calculation will not proceed. This argument bypasses those checks and allows the calculation to proceed anyways. Default: False.