Omar Mohammed

4 Questions 5 Answers 0 Followers

Questions related from Omar Mohammed

How to create psf file from pdb file by VMD?

Hello everybody, I am trying to create psf file from pdb file for a small molecule such as a drug by using the Automatic PSF builder of VMD software. However, I am ending always with the attached...

28 July 2022 5,929 3 View

What is the proper RMSD value to study protein-ligand interaction using MDs?

I am studying protein-ligand interaction using Molecular Dynamics simulations. I have run MDs for the protein alone and the protein with different ligands. RMSD of the protein alone is around 0.39...

03 February 2020 3,411 1 View

Which Chi square value I should choose: closest value to 1 or the lowest one?

I have different conformations, created by MDs, representing a protein. I have compared them with SAXS data by using Crysol. some of Chi square values obtained from Crysol are 0.04, 0.036, 0.034,...

22 January 2020 1,648 5 View

Computer for Gromacs (Molecular dynamic simulation)

I am trying to buy a computer for molecular dynamic studies performed by Gromacs. I have found this computer in the market ThinkPad P17 Mobile Workstation. Do you think it is not good enough to...

01 January 1970 7,507 5 View