OpenMM In ParmEd

This page describes how you can use native Amber or CHARMM force field definition and structure files using the OpenMM application layer in ParmEd or using the API in your own Python programs.

Using the ParmEd Interpreter

Several ParmEd commands have been written using the OpenMM integration built into the underlying classes. The following commands are currently implemented using the OpenMM application layer:

1. OpenMM — This action emulates the sander and pmemd command-lines and will read Amber-style input files (mdin, inpcrd, etc.) and write Amber-style output files (NetCDF or ASCII trajectory, and mdout/mdinfo files with similar information in a different format).
2. energy — This action will compute the molecular mechanical energy using OpenMM for the force field defined by the loaded topology file.

Loading Amber topology files

On the command-line, you can use the -p flag with ParmEd to load an Amber topology file or you can use the parm command inside a ParmEd script or inside the interpreter itself. For example, the following examples accomplish the same task:

bash$ parmed.py -p protein.parm7

Using AMBER Files

Using CHARMM Files