pestifer

Pestifer is a versatile system-preparation tool that facilitates the use of the VMD tool psfgen to generate CHARMM-force-field compatible PSF and PDB files for use in the MD simulation package NAMD. Pestifer automates and extends the standard psfgen/VMD workflow using a simple YAML interface to provide a versatile and user-friendly way to set up molecular dynamics simulations.

Pestifer includes the CHARMM36 force field files from the MacKerell Lab (February 2026 (default), July 2024 (optional)).

Note

Pestifer is under active development. Pestifer development is supported in part by Grants GM100472, AI154071, and AI178833 from the NIH.

Contents

• Introduction
  • Why Pestifer?
  • Why YAML?
  • A partial list of things Pestifer can do
  • Who is Pestifer not for?
  • Why “Pestifer”?
• Installation
  • Software Prerequisites
  • Installation
• Usage
  • Command-line Usage
  • Subcommands
  • Using a custom CHARMM stream file for a small molecule
  • Use in VMD scripts
• Examples
  • BPTI Series (Examples 1–4)
  • Small Proteins (Examples 5–6)
  • HIV-1 Env Ectodomains (Examples 7–12)
  • Insulin Systems (Examples 13–14)
  • SARS-CoV-2 Spike (Example 15)
  • Membrane-Embedded Systems (Examples 16–17)
  • Diverse Applications (Examples 18–22)
• Configuration File Reference
  • charmmff
  • psfgen
  • namd
  • paths
  • tasks
• API
  • pestifer package
• Tcl sources
  • Top-level scripts
  • Tcl scripts
  • Tcl packages
• Changelog
  • [Unreleased]
  • [2.5.2] - 2026-05-28
  • [2.5.1] - 2026-05-28
  • [2.5.0] - 2026-05-18
  • [2.4.13] - 2026-05-14
  • [2.4.12] - 2026-05-13
  • [2.4.11] - 2026-05-13
  • [2.4.10] - 2026-05-11
  • [2.4.9] - 2026-05-11
  • [2.4.8] - 2026-05-11
  • [2.4.7] - 2026-05-11
  • [2.4.5] - 2026-05-11
  • [2.4.4] - 2026-04-28
  • [2.4.3] - 2026-04-28
  • [2.4.2] - 2026-04-28
  • [2.4.1] - 2026-04-27
  • [2.4.0] - 2026-04-27
  • [2.3.1] - 2026-04-24
  • [2.3.0] - 2026-04-24
  • [2.2.11] - 2026-04-24
  • [2.2.10] - 2026-04-20
  • [2.2.9] - 2026-04-20
  • [2.2.7] - 2026-04-19
  • [2.2.6] - 2026-04-19
  • [2.2.5] - 2026-04-18
  • [2.2.4] - 2026-04-18
  • [2.2.3] - 2026-04-17
  • [2.2.0] - 2026-03-04
  • [2.1.9] - 2026-03-03
  • [2.1.8] - 2026-02-18
  • [2.1.7] - 2025-11-19
  • [2.1.6] - 2025-10-22
  • [2.1.5] - 2025-10-22
  • [2.1.4] - 2025-10-12
  • [2.1.3] - 2025-10-10
  • [2.1.2] - 2025-09-30
  • [2.1.1] - 2025-09-23
  • [2.1.0] - 2025-09-19
  • [2.0.3] - 2025-09-15
  • [2.0.1] - 2025-09-04
  • [1.21.2] - 2025-07-17
  • [1.21.1] - 2025-07-15
  • [1.20.3] - 2025-07-14
  • [1.19.1] - 2025-07-11
  • [1.18.1] - 2025-07-08
  • [1.17.0] - 2025-07-05
  • [1.16.3] - 2025-07-03
  • [1.15.1] - 2025-06-22
  • [1.14.1] - 2025-06-18
  • [1.13.3] - 2025-06-17
  • [1.13.2] - 2025-06-16
  • [1.12.1] - 2025-06-04
  • [1.12.0] - 2025-06-03
  • [1.11.2] - 2025-05-27
  • [1.10.0] - 2025-03-27
  • [1.9.0] - 2025-03-27
  • [1.8.3] - 2025-03-19
  • [1.8.2] - 2025-03-11
  • [1.8.1] - 2025-03-10
  • [1.8.0] - 2025-03-07
  • [1.7.4] - 2025-02-23
  • [1.7.2] - 2025-02-12
  • [1.7.1] - 2025-02-10
  • [1.6.1] - 2025-06-29
  • [1.5.9] - 2025-01-22
  • [1.5.6] - 2025-01-03
  • [1.5.4] - 2024-11-05
  • [1.5.3] - 2024-09-30
  • [1.5.2] - 2024-09-24
  • [1.4.8] - 2024-09-24
  • [1.4.7] - 2024-09-18
  • [1.4.4] - 2024-07-10
  • [1.4.3] - 2024-07-02
  • [1.4.2] - 2024-06-27
  • [1.4.1] - 2024-05-16
  • [1.4.0] - 2024-04-01
  • [1.3.9] - 2024-03-04
  • [1.3.8] - 2024-02-29
  • [1.3.7] - 2024-02-29
  • [1.3.5] - 2024-02-26
  • [1.3.4] - 2024-02-06
  • [1.3.3] - 2024-01-31
  • [1.3.2] - 2024-01-24
  • [1.3.1] - 2024-01-12
  • [1.3.0] - 2024-01-11
  • [1.2.9] - 2023-12-19
  • [1.2.8] - 2023-12-05
  • [1.2.5] - 2023-11-28
  • [1.2.3] - 2023-11-20
  • [1.2.0] - 2023-11-16
  • [1.1.2] - 2023-11-09
  • [1.0.9] - 2023-11-07
  • [1.0.6] - 2023-10-31
  • [1.0.1] - 2023-09-20