PyTopol

Reza Salari - Brannigan Lab

Introduction

PyTopol provides utilities to convert certain molecular topologies. It follows a different approach than the force-field conversion tools and is intended to convert the full-topology of a molecule from one format to another. This allows conversion of custom-parameterized topologies across MD packages.

Currently PyTopol includes the following utilities:

• psf2top.py : for converting CHARMM psf files to GROMACS topology format. The reverse conversion of GROMACS topologies to NAMD is planned an will be implemented. Also see here.

Current stage

Current version is 0.1.7.

All 0.1.x versions will be considered alpha. See the results for the current tests below.

Feedback

If you have a question, found a bug or have a suggestion, please submit it here.

License

PyTopol is licensed under GNU GPLv3.

Quickstart

Installation

How to install PyTopol

PSF to GROMACS topology conversion

How to use psf2top.py

Table 1. Summary of the rmsd of potential energy terms between GROMACS 4.6.3 and NAMD 2.9 (kcal/mol). Single and double correspond to the single and double-precision versions of GROMCAS.

--------------------------  -----------------  -----------------
              natoms  ff    GMX-NAMD (double)  GMX-NAMD (single)
--------------------------  -----------------  -----------------
  AD peptide      22  CH27             0.000               0.000
   POPC memb    9916  CH36             0.002               0.021
   DOPC memb   10488  CH36             0.005               0.014
    Lysozyme    1966  CH27             0.009               0.010
 Cholesterol      74  CH36             0.000               0.000
 Pr+Chol+Lip   27562  CH36             0.046               3.988
--------------------------  -----------------  -----------------

For the detailed results, please see here.

Contribution

There are many ways you can help to improve PyTopol:

• Convert your psf files to GROMACS format and compare NAMD and GROMACS energies. Use the issues page to let me know of the potential discrepancies.

• Run simulations using the generated topologies and see if the results make sense.

• Fork this repo, implement improvements and send me a pull request.

Acknowledgement

• Energy conversion factors are from charmm2gromacs-pvm.py script by Par Bjelkmar, Per Larsson, Michel Cuendet, Berk Hess and Erik Lindahl.

Similar tools

• charmm2gromacs is a tool for converting CHARMM force field to GROMACS.
• psfgen-top patches for psfgen (NAMD 2.7 and 2.8) to create gromacs topology.
• SwissParam converts mol2 format to CHARMM and GROMACS formats.