Sultan Khan

4 Questions 2 Answers 0 Followers

Questions related from Sultan Khan

Is it ok for getting a high RMSD in MD simulation?

hello I have done a 50ns MD simulation production run on three different protein-peptide complexes. unfortunately, I am getting quite a high RMSD in all of them. I tried many things but couldn't...

25 July 2023 1,599 2 View

Getting a high RMSD in protein-ligand MD simulation is ok ?

I've done a 50 ns protein-ligand MD simulation. Getting stable RMSD for the first 20 ns, but it increases afterwards, and at some point frame, it's getting very high. My question is, is my md...

20 June 2023 1,148 3 View

What parameter in protein-ligand MD simulation decides number of frames in the simulation output ?

I've done 2ns protein-ligand MD simulation in two ways 1. first I used general MD simulation, generating every single file by commands as suggested in gromacs tutorial. As an output, I've got 200...

05 June 2023 9,402 4 View

Is that necessary to predict antigenicity and allergenicity of epitopes?

Hi, Well, epitopes that bind with MHC are considered antigenic. my question is what is the need to predict antigenicity or allergenicity? I mean if we have predicted epitope data and we know...

07 October 2022 1,596 2 View