Pestifer

NAMD System Preparation Tool

tests PyPI Python License: MIT Docs PyPI Downloads DOI

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.
  • Import & edit an existing system — bring in a PSF built elsewhere (CHARMM-GUI, another tool, an earlier run) and check every atom type and bonded term against the build's CHARMM release before any MD runs, then edit it in place — patches, disulfides, links, glycan grafts — or re-segment and rebuild it for mutations, insertions, and deletions.
  • 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 on an orthohexagonal lattice and protein embedding with any lipid that has a PDB, oriented to the membrane normal, with pierced-ring resolution. Asymmetric leaflets are calibrated one composition at a time, each leaflet's phase (liquid-ordered or liquid-disordered) is a build-time input rather than something the MD has to discover, and every barostatted stage stops on measured density and area convergence instead of a fixed step count.
  • 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.
  • Restartable builds — a run manifest records each task's spec and the state it produced, so an interrupted build resumes from the last cleanly-completed task; change the config and it re-runs from the first task whose spec changed.
  • 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.

Project links

Data verified by PyPI on Aug 14, 2026
Data provided by the project maintainers, verified at the time the release was uploaded to PyPI.

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Newer release available (3.19.1)

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for cameronabrams from gravatar.com cameronabrams

Credits

PyPI data
Data sourced directly from PyPI's database.

Author: Cameron F Abrams

GitHub Statistics

Data verified by PyPI on Aug 14, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License

MIT License

Requires

Python >=3.12

Provides Extra

ligand-paramgen test

Classifiers

Report project as malware

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

pestifer-3.16.2.tar.gz (10.1 MB view details)

Uploaded Source

Built Distribution

If you're not sure about the file name format, learn more about wheel file names.

pestifer-3.16.2-py3-none-any.whl (10.2 MB view details)

Uploaded Python 3

File details

Details for the file pestifer-3.16.2.tar.gz.

File metadata

  • Download URL: pestifer-3.16.2.tar.gz
  • Upload date:
  • Size: 10.1 MB
  • Tags: Source
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/7.0.0 CPython/3.13.14

File hashes

Hashes for pestifer-3.16.2.tar.gz
Algorithm Hash digest
SHA256 71d163b579fabe8cb639a65f678f0aba68d14e3290010f782fef171785090f3e
MD5 0f88f251ba6fda1c55030bd0e21fc8fc
BLAKE2b-256 4efeb457ad7b21fc5b629da6033da0a4ebf2b8b6a8597c0ff935479f49fa37c4

See more details on using hashes here.

Provenance

The following attestation bundles were made for pestifer-3.16.2.tar.gz:

Publisher: release.yaml on cameronabrams/pestifer

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

File details

Details for the file pestifer-3.16.2-py3-none-any.whl.

File metadata

  • Download URL: pestifer-3.16.2-py3-none-any.whl
  • Upload date:
  • Size: 10.2 MB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/7.0.0 CPython/3.13.14

File hashes

Hashes for pestifer-3.16.2-py3-none-any.whl
Algorithm Hash digest
SHA256 3015bf33a4044f07fec78555e42113f78769e1e265a9ee0047fc78a908660683
MD5 dd735c1b9b025cc071a3302a7a3989e3
BLAKE2b-256 43a5ce93de9f77e1d8a197a8231ba0c6b44e7a1d07238be06cbf054e7622d0da

See more details on using hashes here.

Provenance

The following attestation bundles were made for pestifer-3.16.2-py3-none-any.whl:

Publisher: release.yaml on cameronabrams/pestifer

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

Release history Release notifications | RSS feed

3.19.1

2 files

3.19.0

2 files

3.18.0

2 files

3.17.0

2 files

This release

3.16.2 This release

2 files

3.16.1

2 files

3.16.0

2 files

3.15.4

2 files

3.15.3

2 files

3.15.2

2 files

3.15.1

2 files

3.15.0

2 files

3.14.0

2 files

3.13.0

2 files

3.12.0

2 files

3.11.1

2 files

3.11.0

2 files

3.10.1

2 files

3.10.0

2 files

3.9.0

2 files

3.8.0

2 files

3.7.2

2 files

3.6.0

2 files

3.5.0

2 files

3.4.0

2 files

3.3.0

2 files

3.2.1

2 files

3.2.0

2 files

3.1.0

2 files

3.0.1

2 files

3.0.0

2 files

2.9.0

2 files

2.8.0

2 files

2.7.2

2 files

2.7.1

2 files

2.7.0

2 files

2.6.3

2 files

2.6.2

2 files

2.6.1

2 files

2.6.0

2 files

2.5.2

2 files

2.5.1

2 files

2.5.0

2 files

2.4.13

2 files

2.4.12

2 files

2.4.11

2 files

2.4.10

2 files

2.4.9

2 files

2.4.8

2 files

2.4.4

2 files

2.4.3

2 files

2.4.2

2 files

2.4.1

2 files

2.4.0

2 files

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Depot Continuous Integration Fastly CDN Google Download Analytics Sentry Error logging StatusPage Status page