CHARMM Parser

NOMAD Laboratory CoE parser for CHARMM

Version 0.0.2

This is the parser for CHARMM (Chemistry at HARvard Macromolecular Mechanics) code in CHARMM.

Features

• All input and output files are expected to be in the supplied directory and its subdirectories.
• The parser searches for the main input file for extraction more information of the order of the commands and input CARDS. The main input file is assumed to hold at least 80% of the commands given to charmm main process.
• MINI, DYNA, ENER, GETE, PRINT, OPEN, READ, and WRITE commands can be prossesed with this parser.
• Any new MINI, DYNA, ENER, GETE commands are assumed to be a new simulation and each simulation is given in a new section_run in standardized meta information of NOMAD.
• Parser can extract topology information from PSF, RTF, PAR files and CARDS through MDDataAccess package.
• SEQ CARDS can be read only for additional information if topology information is not complete.
• Additional topology information can also be extracted from COOR, CRD files(ascii) and CARDS.
• Input and output coordinates are mainly extracted from both ascii and binary COOR and CRD files/CARDS and PRINT COOR commands. ...The coordinate information of the most recent command before any given command in the second item of this list is assumed to be the input coordinates of the simulation. Similarly, the next PRINT, WRITE command after each simulation is also assumed to be the output coordinates if trajectory data (IUNCRD or IUNWRI units) are missing.
• Trajectory of the simulations are also accessed through MDDataAccess package of python-common.

Download and Installation

The official version lives at:

git@gitlab.mpcdf.mpg.de:nomad-lab/parser-charmm.git

You can browse it at:

https://gitlab.rzg.mpg.de/nomad-lab/parser-charmm

It relies on having the nomad-meta-info and the python-common repositories one level higher. The simplest way to have this is to check out nomad-lab-base recursively:

git clone --recursive git@gitlab.mpcdf.mpg.de:nomad-lab/nomad-lab-base.git

This parser will be in the directory parsers/charmm of this repository.

Running and Testing the Parser

Requirements

The required python packages can be installed with (see python-common):

pip install -r nomad-lab-base/python-common/requirements.txt

Usage

CHARMM MD log output files can be parsed with:

python CHARMMParser.py [path/toFile]

Test Files

Example log output files of CHARMM can be found in the directory test/examples. More details about the calculations and files are explained in the README file under examples directory.