PyGBe: Python GPU code for Boundary elements

This is a boundary element method code that does molecular electrostatics calculations with a continuum approach. It calculates solvation energies for proteins modeled with any number of dielectric regions. We use the formulation presented in the paper by Yoon and Lenhoff: "A Boundary Element Method for Molecular Electrostatics with Electrolyte Effects", Journal of Computational Chemistry, Vol. 11, No. 9, 1990. Proper user guide is under development.

This code is accelerated using the Barnes-Hut treecode so that each GMRES iteration scales as O(NlogN). The code is written in Python putting the most computationally intensive parts on the GPU, interfacing with PyCUDA, and some parts are wrapped in C++ using SWIG.

Installation

The following instructions assume that the operating system is Ubuntu. Run the corresponding commands in your flavor of Linux to install.

Dependencies (last tested)

• Python 2.7.11
• Numpy 1.10.4
• SWIG 3.0.8
• NVCC 7.0
• PyCUDA 2015.1.3

Python and Numpy

To install the specific version of these packages we recommend using either conda or pip.

SWIG

To install SWIG we recommend using either conda, your distribution package manager or SWIG's website.

NVCC

Download and install the CUDA Toolkit.

PyCUDA

PyCUDA must be installed from source. Follow the instructions on the PyCUDA website. We summarize the commands to install PyCUDA on Ubuntu here:

> cd $HOME
> mkdir src
> cd src
> wget https://pypi.python.org/packages/source/p/pycuda/pycuda-2015.1.3.tar.gz
> tar -xvzf pycuda-2015.1.3.tar.gz
> cd pycuda-2015.1.3
> python configure.py --cuda-root=/usr/local/cuda
> make
> sudo make install 

If you are not installing PyCUDA systemwide, do not use sudo to install and simply run

> make install

as the final command.

Test the installation by running the following:

> cd test
> python test_driver.py

PyGBe has been run and tested on Ubuntu 12.04, 13.10 and 15.04.

Installing PyGBe

Create a clone of the repository on your machine:

> cd $HOME/src
> git clone https://github.com/barbagroup/pygbe.git
> cd pygbe
> python setup.py install clean

If you are installing PyGBe systemwide (if you installed PyCUDA systemwide), then use sudo on the install command

> sudo python setup.py install clean

Run PyGBe

PyGBe cases are divided up into individual folders. We have included a few example problems in examples. Additional problem folders can be downloaded from coming soon.

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 run any PyGBe case, you can pass pygbe a relative or an absolute path to the problem folder.

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).

AMOEBA support

This version of PyGBe comes with support for the polarizable multipolar force field AMOEBA. If you are using this force field, add the --polarizable flag to your running command. For example:

> pygbe examples/1pgb_amoeba --polarizable

The required input files for AMOEBA change a little bit, as it doesn't use the .pqr file anymore:

1. You need to have a .xyz file with the atom positions. You can obtain that from a PDB file with the program pdbxyz from the Tinker package.
2. AMOEBA uses a .key file with the parameterization of the protein (charge distribution, radii, polarizability, etc.). You can include those parameters directly in the .key file or have it point to a predefined parameter file, like amoebapro13.prm. If you choose to point to a .prm file, the path can be either absolute or relative to the folder with the problem.
3. The name of the .key and .xyz files need to match, and that file name (without extension) has to be under charge_file in the .config file.

You can still use msms for meshing. To get the .xyzr file for msms run the Python script under scripts/tinker_to_xyzr.py with the name of the .key file (without extension) as input.

Let us know if you have any questions/feedback.

Enjoy!

Christopher (christopher.cooper@usm.cl)