Smit Patel

7 Questions 5 Answers 0 Followers

Questions related from Smit Patel

How to fix pbc problem for protein-membrane system?

I ran a 100ns molecular dynamics simulation of a protein-membrane system where the protein is 10 angstroms away from the membrane. After concatenating the trajectory files and performing...

13 August 2024 5,251 5 View

How to create a config file for calculate the protein pocket volume in CAVER 3.0?

Hello all, I have 1000 frames and i want to calculate the binding pocket volume of the protein using CAVER 3. Can someone help regarding the creation of configuration file for the same to execute...

31 March 2023 4,860 0 View

How to interpret the shamlog.log file?

hello all, I'm trying to make a free energy landscape plot for my protein. After using gmx sham i got two files shamlog.log and bindex.ndx. I am unable to understand which bin will have the...

14 February 2023 9,900 0 View

What are the prerequisites before performing principal component analysis in md simulation?

hello all, I'am performing a 1000ns simulation for my protein and want to observe it's dynamic motion of domains through PCA analysis. i have two questions: 1) do we have to remove the PBC...

10 February 2023 2,285 4 View

What is the best tool for analysis of binding pocket volume in the trajectory file?

hello all, I'm new to MD simulation and want to analyze the pocket volume during the trajectory. Is there any tool which can perfectly predict the same. I used POVME program to find the volume,...

29 November 2022 6,237 0 View

How to find out the number of water molecules in the active site of the protein?

hello all, i'm trying to find out the number of water molecules in the binding site of the protein across a 100ns trajectory file(.xtc). i'm new to programing and simulations, I followed how to...

01 November 2022 4,738 1 View

What are the steps needed to find the PCA of protein-ligand complex?

hello all, I have a 100ns sim .xtc file for a protein ligand complex. for the calculation of the pca i first center the complex applied rotational and translational fitting gmx trjconv and then...

01 November 2022 6,163 0 View