BrownDyeTools

BrownDye plugin for Pymol

This Pymol plugin allows setting up, running and analyzing Brownian dynamics simulation using the BrownDye collection of applications. This plugin can also be used as a standalone GUI, without Pymol.

Requirements

• PDB2PQR Download and install the precompiled binary version of PDB2PQR.

• APBS Download and install the precompiled binary version of APBS.

• BrownDye There is no precompiled binary distribution, you have to download and compile the source code.

Currently only Linux OS is supported. MacOS is untested.

Installation

• Download and install pymol

• Download BrownDyeTools

• Open PyMol and install BrownDyeTools: Plugin -> Manage Plugins -> Install then locate BrownDyeTools.py file.

Using

• Start pymol and open BrownDyeTools plugin: Plugin -> BrownDye Tools

Configuration Tab

• Create a randomly named project directory or browse for a custom directory.

• Set PDB2PQR_PATH, APBS_PATH and BD_PATH locations. If you have these set as environment variables in your shell they will be picked up by the plugin.

PQR files Tab

• Pick molecule 0 and 1 PDB files, or use Pymol selection.

• Press "Create PQR files" to create PQR files from the PDB files using pre-set force field.

• Or load your own PQR files.

APBS Tab

• Press Calculate grid size for both molecule 0 and 1 to get automatic grid dimensions or fill in your customized grid size values.

• Adjust APBS options if necessary and press Run APBS to generate grids to launch two APBS calculation (for molecule 0 and 1). This might take a couple of minutes, depending on the molecule size and your computing hardware.

Reaction criteria Tab

• You can use either the default protein-protein contact file or load your own.

• Adjust the reaction criteria if desired and press Create reaction files to generate the necessary reaction input files.

BD setup Tab

• Adjust - if necessary - BrownDye input file parameters. For detailed description of the input parameters see BrownDye documentation. Get Debye length will automatically fetch the APBS calculated value.

• Press Generate BD input files to create the necessary BrownDye input files. This might take a couple of minutes, depending on the size of molecules 0 and 1.

BD simulation Tab

• You can choose either to run BrownDye simulation within the plugin or send it to background. Obviously, the foreground (in the plugin) execution is appropriate for shorter simulation. When running in the plugin various statistics are updated during the run and displayed.

Analysis Tab

• After simulation is finished you can pick and analyze the created trajectory files. The Analyze button will print how many successful events were recorder in the particular trajectory files and their index numbers. You can then pick one successful trajectory (Select trajectory file) and convert it to XYZ file (Convert to xyz trajectory) and visualize it in Pymol (Load xyz trajectory).

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License

This software is released under the terms of GNU GPL3 license. For more details please see the accompanying documentation.

(c) 2016-19 National Biomedical Computation Resource