scipion-chem-amber

AMBER is a suite of biomolecular simulation programs. Amber is distributed in two parts: AmberTools23 (which is free) and Amber22 (which requires a license).

Warning

This plugin is currently under first-stage development, so you may encounter errors or some options may not be available. Sorry for the inconvenience.

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-amber

• Developer’s version

  1. Download repository:

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

  2. Install:

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

Protocols

• Amber Ligand Parametrization: Parametrizes and prepares a ligand to be used in Amber simulations using pdb4amber and Antechamber.

• Amber System Preparation: Prepares a system for Amber MD simulation, cleaning the input PDB for further analysis and generating topology and coordinate files necessary.

• Amber Molecular Dynamics (MD) Simulation: Defines and executes a Amber MD simulation.