Run PyGBe

PyGBe cases are divided up into individual folders. We have included a few example problems in examples.

Test the PyGBe installation by running the Lysozyme (lys) example in the folder examples. The structure of the folder is as follows:

lys
  ˫ lys.param
  ˫ lys.config
  ˫ built_parse.pqr
  ˫ geometry/Lys1.face
  ˫ geometry/Lys1.vert
  ˫ output/

To run this case, you can use

> pygbe examples/lys

To test PyGBe-LSPR, run the single silver sphere (lspr_silver) example.

To run lspr cases, you can use

> pygbe-lspr examples/lspr_silver

To run any PyGBe case, you can pass pygbe (or pygbe-lspr if it’s a LSPR application) a relative or an absolute path to the problem folder.

Note that PyGBe will grab the first param and config files that it finds in the problem folder (they don’t have to share a name with the folder, but it’s helpful for organization). If you want to explicitly pass in a different/specific param or config file, you can use the -p and -c flags, respectively.

If you have a centralized geometry folder, or want to reuse existing files without copying them, you can also pass the -g flag to pygbe to point to the custom location. Note that this path should point to a folder which contains a folder called geometry, not to the geometry folder itself.

For more information on PyGBe’s command line interface, run

> pygbe -h

or

> pygbe-lspr -h

Mesh:

In the examples folder, we provide meshes and .pqr files for a few example problems. To plug in your own protein data, download the corresponding .pdb file from the Protein Data Bank, then get its .pqr file using any PDB to PQR converter (there are online tools available for this). Our code interfaces with meshes generated using MSMS (Michel Sanner’s Molecular Surface code).

The meshes for the LSPR examples and some Poisson Boltzmann that involve spheres, where generated with a script called mesh_sphere.py located in pygbe/preprocessing_tools/.

In Generate meshes and pqr you can find detailed instructions to generate the pqr and meshes.

Input and Parameter files:

You can find detailed instructions to generate these files in the Input Files section.

Performance:

A short notebook outlining performance gains vs APBS is available here: PyGBe Performance