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.

Key capabilities

• Fully local & reproducible — a single YAML config plus a pinned pestifer version is a complete record of how a system was built; no data ever leaves your machine.
• Broad structure input — build from RCSB PDB IDs, local PDB/mmCIF files, or AlphaFold models, with automatic construction of biological assemblies.
• Simulation-ready CHARMM36 output — generate PSF/PDB/xsc for NAMD from the bundled CHARMM36 force field, including glycoproteins and nucleic acids.
• Sequence & structure edits — mutations, insertions, deletions, substitutions, residue patches, chain cleavage and relabeling, fusions, and arbitrary backbone/side-chain rotations.
• Loop & gap modeling — build unresolved internal loops and ligate chain breaks.
• Glycan grafting — transplant glycans from a donor structure with automatic clash and ring-piercing resolution.
• Membrane building — fast grid-based bilayers and protein embedding with any lipid that has a PDB, oriented to the membrane normal, with pierced-ring resolution.
• Solvation & ionization — TIP3P water or non-water solvents, with on-demand generation and caching of missing solvent boxes and lipid conformers.
• Custom ligands — use CGenFF-parameterized small molecules, plus a workflow to contribute your own residue definitions.
• Merge & package — combine pre-built systems (auto-resolving segment/chain collisions) and emit ready-to-run NAMD configs, SLURM restart scripts, solvent-stripped PSF/DCD, and plots of NAMD-log time series.

Installation

pip install pestifer

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

Pestifer also requires access to the following executables:

1. namd3 and charmrun
2. vmd and catdcd

Pestifer includes a mirrored copy of the Feb 2026 Charmm36 force field, plus a few local corrections to upstream files and some added residue/ligand/ion definitions — see CHARMM force-field customizations for the full list and rationale.

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

Pestifer is developed on GitHub at https://github.com/cameronabrams/pestifer.

Code changes:

1. Fork, clone, and install editable: pip install -e .
2. Branch, make your change, and add tests.
3. Run the suite: pytest (or uv run pytest).
4. Add a bullet under ## [Unreleased] in CHANGELOG.md.
5. Push and open a Pull Request.

Content contributions — a new example, a PDB-repository entry, or a custom CHARMM residue — use the modify-package subcommand, which makes the branch, commits exactly the files it touches, and prints the push / PR steps for you (no manual branching needed). See the modify-package documentation.