PARMED

ParmEd


Synopsis

A tool for aiding in investigations of biomolecular systems using molecular simulation packages (Amber, CHARMM, and OpenMM)

Description

ParmEd is a general tool for aiding in investigations of biomolecular systems using popular molecular simulation packages, like Amber, CHARMM, and OpenMM written in Python.

What is it? There are two parts to ParmEd – the Python API that exposes the core classes used in its modeling capabilities, and two front-end Python programs (parmed and its GUI counterpart, xparmed) that make use of the ParmEd API to allow rapid prototyping and parameter-topology modifications for use in molecular simulations.

Why use it? You can use it for a variety of modeling purposes, like manipulating system topologies (i.e., the atoms, bonds, and other bonded terms like valence angles) and translating between file formats (e.g. PDB, mmCIF/PDBx, Amber prmtop, and CHARMM psf) and even other APIs (e.g. PyRosetta). What sets ParmEd apart from tools like OpenBabel is that it stores and tracks force field parameters so that the resulting files can be used to carry out molecular mechanics simulations with tools like Amber, OpenMM, NAMD, and CHARMM.

ParmEd has sophisticated machinery built into its core classes that substantially reduces the burden of bookkeeping when manipulating chemical structures (for instance, adding or deleting an atom from a structure automatically updates the indices in each of the parameter arrays defining the system topology so you don’t have to worry about it).

URL

http://parmed.github.io/ParmEd/html/index.html

Versions

NMRbox Version Software Version
3.0.0 Downloaded_07-24-17,

Keywords

  • Molecular Dynamics
  • Utilities