Puneet Kumar

5 Questions 10 Answers 0 Followers

Questions related from Puneet Kumar

How to find the exact amino acid positions of different domains (e.g., propeller, hybrid, etc.) in an Integrin?

I wish to highlight the structural domains in the integrin receptors for which I need exact amino acid's location (start and end). Literature has mentioned the different domain names, but not...

15 March 2023 6,532 0 View

Analysis of Desmond output file in Gromacs?

I have the output (-out.cms) file of the protein ligand simulation from Desmond. I wish to analyse some different aspects of the obtained Desmond output file in Gromacs. What are the necessary...

28 February 2023 9,738 0 View

Error using MPI on HPC?

I am trying to run a protein-ligand MD simulation using slurm script on the HPC system. But I am getting the following error (screenshot attached). Any suggestion to solve this error would be...

09 December 2022 174 3 View

Error encountered while calculating the Z-score and Energy plot in ProSA-web?

Hello everyone! I used Schrodinger Prime to predict a protein structure (sequence identity with template ~71%). Knowledge-based model building method was used to generate the output model. While...

12 October 2019 5,589 22 View

What are the other computational study that can be performed on Modeled protein?

I have modeled a protein, performed MD simulation and Docking studies. What are the other/additional computational study that can be performed further in order to target a high impact journal.

17 April 2019 236 6 View