Installation¶

Software Prerequisites¶

The commands vmd (v. 1.9.4 or better; v. 2.0.0 or better recommended), charmrun, catdcd (v. 5.2 required), and namd3 (v. 3.0.2 recommended) should be in your path. By default, Pestifer expects your GPU-enabled namd3 to be in your path as namd3gpu. To build membrane systems using Pestifer’s packmol integration, you must have packmol (v. 20.15.1 or better) in your path too.

Note

catdcd version 5.2 or later is required. Earlier versions silently drop insertion codes from residue identifiers when reading and writing DCD trajectory files. Pestifer uses insertion codes to distinguish residues that share the same sequence number (a common occurrence in antibody structures and other proteins with non-standard numbering), so an older catdcd will corrupt coordinate data for those systems without any warning.

Note

packmol and conda environments. AmberTools ships a packmol binary as part of packmol-memgen, and any active conda environment that has AmberTools installed will put that (older) packmol at the front of your PATH. Pestifer will refuse to run with it because it predates the pbc keyword.

Bash aliases (alias packmol=/usr/local/bin/packmol) do not help here, because pestifer launches packmol from a non-interactive subprocess where shell aliases are not expanded.

Recommended best practice:

Download packmol >= 20.15.1 from the m3g/packmol GitHub repository and build it.
Install the resulting binary somewhere stable outside any conda environment, e.g. /usr/local/bin/packmol.
Tell pestifer to use that binary by setting paths.packmol in your run YAML:
```
paths:
  packmol: /usr/local/bin/packmol
```

The paths.packmol setting is an absolute path that bypasses PATH resolution entirely, so it cannot be shadowed by conda activation.

Installation¶

To use Pestifer, install it from PyPI:

$ pip install pestifer

Pestifer is under very active development. To get the latest version, just update:

$ pip install -U pestifer

If you want a bleeding-edge, potentially unstable version, or you just want the source code, you can clone it from GitHub:

$ git clone git@github.com:cameronabrams/pestifer.git
$ cd pestifer
$ pip install -e .

Of course, you need to pull changes from the repository periodically to keep up with the latest development. Commits tagged as releases are typically stable. Consider forking the repository if you want to make changes or contribute to the project.