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.
pip install pestifer
Once installed, the user has access to the main pestifer command.
Pestifer also requires access to the following executables:
namd2 and charmrunvmd and catdcdpackmolBy 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.
Please visit readthedocs for full documentation.
See the CHANGELOG for full details.
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.
git checkout -b feature/fooBar)git commit -am 'Add some fooBar')git push origin feature/fooBar)FAQs
A NAMD topology/coordinate input builder
We found that pestifer demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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