pdb2oniom

A python implementation of pdb2oniom for QM/MM (ONIOM) calculations.

An alternative of pdb2oniom perl script originally developed at TAO package. The feature to import force field parameters from an input parm7 file is inspired by the CATs package and its topcrd2mmcom command.

Feature

• Generate a Gaussian input file for ONIOM calculations from AMBER topology (.parm7) and restart (.rst7) files.
• The force field parameters in the AMBER topology file will be written in the output gjf file automatically.

Installation

# If you are using python3.12 or higher (e.g. Ubuntu 24.04), create and activate venv at first.
# "/path/to/workingdirectory" is your working directory.
mkdir -p /path/to/workingdirectory ; cd /path/to/workingdirectory
python3.12 -m venv .venv
source .venv/bin/activate
python3.12 -m pip install numpy==1.26.5 ParmEd==4.3.0

# install from GitHub
python3.12 -m pip install git+https://github.com/BILAB/pdb2oniom.git
# upgrade
python3.12 -m pip uninstall pdb2oniom -y && python3.12 -m pip install --upgrade git+https://github.com/BILAB/pdb2oniom.git

Usage

An example to run:

$ pdb2oniom_py -p init.parm7 -r init.rst7 --resid corelist.txt -n 7

2024-01-29 15:34:52,406 pdb2oniom.py:782 - INFO - pdb2oniom.py ver.0.3.2: Amber parm and rst7 files to Gaussian ONIOM input file.
2024-01-29 15:34:53,456 pdb2oniom.py:691 - INFO - Total charge of low layer is calculated -18
2024-01-29 15:34:53,456 pdb2oniom.py:692 - INFO - Core residues list file corelist.txt provided.
2024-01-29 15:34:53,456 pdb2oniom.py:693 - INFO - All residues within 7.0 Å from core region are free to move (0) during geometry optimization.
2024-01-29 15:34:53,523 pdb2oniom.py:146 - INFO - 2289 atoms are set to be movable during geometry optimization.
2024-01-29 15:34:54,790 pdb2oniom.py:705 - INFO - Opening file newinput.gjf for output ...
2024-01-29 15:34:54,795 pdb2oniom.py:708 - INFO - Successfully wrote newinput.gjf file.
2024-01-29 15:34:54,795 pdb2oniom.py:709 - INFO - Opening file newinput.gjf.onb for output ...
2024-01-29 15:34:54,799 pdb2oniom.py:713 - INFO - Successfully wrote newinput.gjf.onb file.
2024-01-29 15:34:54,799 pdb2oniom.py:714 - INFO - pdb2oniom.py ends.

2024-01-29 15:34:54,799 pdb2oniom.py:715 - INFO - NOTE: The charges and multiplicity of high layer should be modified for your calculations. Please use GaussView 6 to modify the QM regions and link atoms.