pestifer

Pestifer

NAMD System Preparation Tool

Pestifer is a fully automated simulation-ready MD system preparation tool, requiring as inputs only biomolecular structures (e.g., PDB IDs, PDB files, mmCIF files, alphafold IDs) and a handful of customization parameters, to generate NAMD-compatible input files (PSF, PDB, and xsc). It is basically a highly functionalized front end for VMD's psfgen utility. It also has a few handy subcommands for working with NAMD output.

Installation

pip install pestifer

Once installed, the user has access to the main pestifer command.

Pestifer also requires access to the following executables:

• namd2 and charmrun
• vmd and catdcd
• packmol

By default, pestifer looks for these commands in your path. Specific paths for these can be stipulated in the paths directive of your input file.

Pestifer includes the July 2024 Charmm36 force field.

Documentation

Please visit readthedocs for full documentation.

Version History

See the CHANGELOG for full details.

Meta

https://github.com/cameronabrams

Pestifer is maintained by Cameron F. Abrams

Pestifer is distributed under the MIT license. See LICENSE for more information.

Pestifer was developed with support from the National Institutes of Health via grants GM100472, AI154071, and AI178833.

Contributing

• Fork it (https://github.com/cameronabrams/pestifer/fork)
• Create your feature branch (git checkout -b feature/fooBar)
• Commit your changes (git commit -am 'Add some fooBar')
• Push to the branch (git push origin feature/fooBar)
• Create a new Pull Request