VMD allows converting PDB to PSF format but sometimes it gives multiple errors. Therefore, in this article, we are going to convert PDB into PSF format using a different method.

We will use the ParmEd [1] package for that. You can download and install this package from here.

Let’s say we have a PDB file named, prot.pdb that we are trying to convert into PSF format.

#!/usr/bin/env python3

import parmed as pmd

structure = pmd.load_file('prot.pdb')

structure.save('prot.psf')

Save this file in Python format and run it. This will output ‘prot.psf’ file that you can also use in VMD.

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1. Shirts, M.R., Klein, C., Swails, J.M. et al. (2017). Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. J Comput Aided Mol Des 31, 147–161.