scipion-chem-openmm

OpenMM is a high-performance toolkit for molecular simulation.

Installation

A) Requirements

In order to use this plugin, you need to install first scipion-chem.

B) Installation steps

• Install the stable version

  Through the plugin manager GUI by launching Scipion and following Others >> Plugin Manager, or

scipion3 installp -p scipion-chem-openmm

• Developer’s version

  1. Download repository:

  git clone https://github.com/scipion-chem/scipion-chem-openmm.git

  2. Install:

  scipion3 installp -p /path/to/scipion-chem-openmm --devel

Warning

Installation of the stable version through the Plugin Manager or with the command provided above is not available yet.

Please install the developer version until a stable version is released, or install the latest stable version with the following steps:

cd /path/to/scipion-chem-openmm && git checkout master && scipion3 installp -p . --devel

Protocols

• OpenMM Receptor Preparation: Prepares a protein AtomStruct object using PDBFixer to prepare it for posterior analysis.

• OpenMM System Preparation: Prepares a OpenMMSystem using the OpenMM API, including the preapred receptor and the solvent.

Note

This plugin is currently under development and more protocols will be available soon.