ParmEd

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).

What can it do?

The core parmed package provided as part of ParmEd is intended to provide a powerful, but simple, API for carrying out tasks common in the field of biomolecular simulations. For example, some of its features include:

  • Simply iterate through atoms as well as other parameters found in common molecular mechanical force fields

  • Rapidly modify a system topology and its parameters, and write files that can be used with the Amber and CHARMM program suites (as well as other programs that support those file types, like NAMD)

  • Carry out investigations using force fields, like molecular dynamics, directly on modern, high-performance hardware (like Graphics Processing Units) using the OpenMM library and Python application layer

  • Dimensional analysis with a complete system of physical units

  • Translate between a variety of file formats in common use by various programs including:

    • Amber prmtop, inpcrd, NetCDF trajectory, and NetCDF restart files

    • CHARMM PSF, coordinate, and restart files

    • Gromacs topology and GRO files

    • PDB files, supporting a wide range of dialects that technically violate the PDB standard

    • PDBx/mmCIF files – the new standard for the Protein Data Bank

  • Extract metadata from the PDB and PDBx/mmCIF files, such as citation information and related database entries

Roadmap: Main goals and future directions

One of the main goals of ParmEd is to provide a single interface for all of the various biomolecular simulation programs and file formats out there and provide a platform upon which transferring data between these different formats and programs is easy and, most importantly, reliable.

Every program is different–developed by different people for different purposes to solve perhaps slightly different scientific problems. As such, each program has something to offer that the others don’t, be it a fancy new method, improved computational performance, better force field for a particular molecule, easier simulation setup, etc. It is currently very difficult to combine components of different program suites into a single workflow, however, given the highly specialized nature of the various file formats for the programs they were written around (e.g., the Amber topology file in the Amber programs, the GROMACS top and itp files for GROMACS, etc.).

Some programs out there will allow you to take, for instance, an Amber topology file and convert it into something GROMACS will understand, but the reverse is not available in any tool. ParmEd hopes to bridge this gap in addition to providing a flexible API that will allow you to go beyond what each programs’ modeling tools allow you to do by themselves. It is an ambitious goal, to be sure, but good progress has already been made.

Check out the Github repository and its issue tracker to keep up-to-date with the planned as well as on-going developments!

Slides and presentations

I will post any slides pertaining to ParmEd from talks that I’ve given here, in the hopes that they may be helpful or informative.

Getting Started

When to use ParmEd?

  • When you want to extract information about a structure or parameters from one of the supported file formats.

  • When you want to manipulate molecular mechanical (force field) descriptions of chemical systems to quickly prototype ideas involving Hamiltonian modifications.

  • When you want to manipulate chemical systems by selecting a subset of the atoms.

  • When you want to combine or replicate the contents of one or more chemical systems.

  • When you want to convert molecular mechanical descriptions of molecules from a format that one program supports to another (e.g., converting an Amber topology file to a Gromacs topology file or vice-versa).

  • When you want to carry out molecular dynamics investigations on high-performance computational hardware (like GPUs) using OpenMM

Common examples

The simplest example is to use ParmEd to download and inspect a PDB file. We can find out numerous attributes about a structure defined by a PDB file, like the number of atoms, residues, and even various citation information. For example:

>>> import parmed as pmd
>>> pmd.download_PDB('4lzt')
<Structure 1164 atoms; 274 residues; 1043 bonds; PBC (triclinic); NOT parametrized>
>>> lysozyme = pmd.download_PDB('4lzt')
>>> lysozyme.authors
'M.A.WALSH,T.SCHNEIDER,L.C.SIEKER,Z.DAUTER,V.LAMZIN,K.S.WILSON'
>>> lysozyme.experimental
'X-RAY DIFFRACTION'
>>> len(lysozyme.atoms)
1164
>>> len(lysozyme.residues)
274
>>> # Get all backbone atoms
... lysozyme['@CA,C,N']
<Structure 393 atoms; 135 residues; 386 bonds; NOT parametrized>

A simple example demonstrating the file conversion capabilities is to convert a PDBx/mmCIF file into the more commonly supported PDB format:

>>> import parmed as pmd
>>> pmd.download_CIF('4lzt').save('4lzt.pdb')
>>> # Now read in the PDB file we just created
... pmd.load_file('4lzt.pdb')
<Structure 1164 atoms; 274 residues; 1043 bonds; PBC; NOT parametrized>

Contributing

If you would like to contribute, please head over to the Github repository at https://github.com/ParmEd/ParmEd and feel free to jump right in! New issues and pull requests are always welcome.

If you want to start contributing to the code base, please check out the developer’s documentation for general information about style guides and the like.