Generating input files
Use write_input.py to generate input files for quantum chemistry packages. Currently input files can be created for Gaussian, xTB (through Gaussian), ORCA and Q-Chem. Some of the options for this script are specific to our QM-cluster modelling workflow and may not be relevant to other users.
Make sure to use a model pdb file that has the frozen atom info encoded (see template pdb section above) to ensure the atom constraints are applied properly
Basic usage of write_input.py to create an input file to do a basic geometry optimisation + frequency calculation:
# Example usage of write_input: Gaussian
python3 $HOME/git/RINRUS/bin/write_input.py -pdb model_N_template.pdb -c 2 -format gaussian
# Example usage of write_input: xTB (in Gaussian)
python3 $HOME/git/RINRUS/bin/write_input.py -pdb model_N_template.pdb -c 2 -format gau-xtb
# Example usage of write_input: ORCA
python3 $HOME/git/RINRUS/bin/write_input.py -pdb model_N_template.pdb -c 2 -format orca
# Example usage of write_input: Q-Chem
python3 $HOME/git/RINRUS/bin/write_input.py -pdb model_N_template.pdb -c 2 -format qchem
# Useful arguments for basic usage of write_input:
-pdb FILE pdb file to use as structure in input file
-m MULT model multiplicity
-c LIGCHRG ligand charge
-format PROG software package (gaussian/gau-xtb/orca/qchem)
-intmp FILE input template for selected software package (if none specified, the ones in $HOME/git/RINRUS/template_files/ are used)
-inpn NAME name of input file (default: 1.inp)
-basisinfo 'intmp' (Gaussian only) use basis set info from the input template file instead of the library in $HOME/git/RINRUS/lib3/gaussian_basis_dict.py
Full set of arguments for using write_input.py:
# General arguments:
-m MULT model multiplicity
-c LIGCHRG ligand charge
-format PROG software package (gaussian/gau-xtb/orca/qchem/psi4-fsapt)
-intmp FILE input template for selected software package (defaults to the ones in $HOME/git/RINRUS/template_files/ if none specified)
-inpn NAME name of input file (default: 1.inp or input.dat for psi4-fsapt)
-basisinfo 'intmp' (Gaussian only) use basis set info from the input template file instead of default RINRUS basis set library
-wdir PATH working directory
-type TYPE type of structure processing for input file:
'pdb': use pdb file normally (default)
'hopt': freeze all heavy atoms so only hydrogen atoms optimized
'gauout': take structure from Gaussian output
'replacecoords': update selected atom coords e.g. to create TS guess
# If using -type 'pdb' (default if no type specified) or 'hopt', these are required:
-pdb FILE pdb file
# If using -type 'gauout', these are required:
-tmp FILE template pdb file for creating new pdb from output
-outf FILE Gaussian output file
-ckp FILE Gaussian checkpoint file
# If using -type 'replacecoords', these are required:
-pdb1 FILE starting pdb file
-pdb2 FILE pdb to take coordinates from
-parts FILE text file containing species in pdb1 to be replaced with pdb2 coordinates
# If using -format 'psi4-fsapt', these are required:
-seed SEED seed to define as fragment A, rest of enzyme will be fragment B