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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

How to make swarm boxplot?

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How to make swarm boxplot?

With the new year, we are going to start with a very simple yet complicated topic (for beginners) in bioinformatics. In this tutorial, we provide a simple code to plot swarm boxplot using matplotlib and seaborn. (more…)

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Bioinformatics Programming

How to obtain ligand structures in PDB format from PDB ligand IDs?

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How to obtain ligand structures in PDB format from PDB ligand IDs?

Previously, we provided a similar script to download ligand SMILES from PDB ligand IDs. In this article, we are downloading PDB ligand structures from their corresponding IDs. (more…)

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Bioinformatics Programming

How to obtain SMILES of ligands using PDB ligand IDs?

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How to obtain SMILES of ligands using PDB ligand IDs?

Fetching SMILE strings for a given number of SDF files of chemical compounds is not such a trivial task. We can quickly obtain them using RDKit or OpenBabel. But what if you don’t have SDF files of ligands in the first place? All you have is Ligand IDs from PDB. If they are a few then you can think of downloading SDF files manually but still, it seems time-consuming, especially when you have multiple compounds to work with. Therefore, we provide a Python script that will read all Ligand IDs and fetch their SDF files, and will finally convert them into SMILE strings. (more…)

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