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Bioinformatics Programming

How to convert the PDB file to PSF format?

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How to convert the PDB file to PSF format?

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.


  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.

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

Bioinformatics Programming

vs_analysis_compound.py: Python script to search for binding affinities based on compound names.

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vs_analysis_compound.py: Python script to search for binding affinities based on compound names.

Previously, we have provided the vs_analysis.py script to analyze virtual screening (VS) results obtained from Autodock Vina. In this article, we have provided another script to search for binding affinity associated with a compound. (more…)

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Bioinformatics Programming

How to download files from an FTP server using Python?

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How to download files from an FTP server using Python?

In this article, we provide a simple Python script to download files from an FTP server using Python. (more…)

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Bioinformatics Programming

smitostr.py: Python script to convert SMILES to structures.

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smitostr.py: Python script to convert SMILES to structures.

As mentioned in some of our previous articles, RDKit provides a wide range of functions. In this article, we are using RDKit [1] to draw a molecular structure using SMILES. (more…)

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