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.
  • 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.

Project links

Data verified by PyPI on Jul 29, 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 Jul 29, 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-3.14.0.tar.gz (11.8 MB view details)

Uploaded Source

Built Distribution

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

pestifer-3.14.0-py3-none-any.whl (11.9 MB view details)

Uploaded Python 3

File details

Details for the file pestifer-3.14.0.tar.gz.

File metadata

  • Download URL: pestifer-3.14.0.tar.gz
  • Upload date:
  • Size: 11.8 MB
  • Tags: Source
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/6.1.0 CPython/3.13.14

File hashes

Hashes for pestifer-3.14.0.tar.gz
Algorithm Hash digest
SHA256 42f534602dfdc11effae94f51abdefc421cf9b0a7394c94a6d051e7e6e89776d
MD5 9583e05ceb0a4c5c14c991797ee21d1d
BLAKE2b-256 2b42e2c38f948ae4ed0628de5721acf714d73ede57e498ed64da6e8566e41b76

See more details on using hashes here.

Provenance

The following attestation bundles were made for pestifer-3.14.0.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-3.14.0-py3-none-any.whl.

File metadata

  • Download URL: pestifer-3.14.0-py3-none-any.whl
  • Upload date:
  • Size: 11.9 MB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/6.1.0 CPython/3.13.14

File hashes

Hashes for pestifer-3.14.0-py3-none-any.whl
Algorithm Hash digest
SHA256 17637bb062edcfad73f0f21c98011d0581a82a3cdea0dbed73f166f69e798f17
MD5 e6665dd03fe76e1e91da5056c7c448b6
BLAKE2b-256 4b6b9bf24648345cdbe6385ec19e6a13c5c36b453c9e7052b42a8ff976630d2c

See more details on using hashes here.

Provenance

The following attestation bundles were made for pestifer-3.14.0-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

3.16.2

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

This release

3.14.0 This release

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