stereochemical issue after MD simulation

Question

[singh.bioinfo]

Hi everyone,

I need suggestion from you all. I have performed MD simulation of predicted protein with the help of GROMACS. After completing the simulation, I checked stereo-chemical analysis but I found that the amino acids of simulated protein are more in a disallowed region as compare to initially predicted protein. If simulation gives you structure accuracy so why it does not happen in my experimental case. I hope i will get answer asap. Thanking you

Answer 1

[rprog008]

At first you fix the PDB file of protein via WhatIf server and later perform MD simulation. It generally work. :)