Question: stereochemical issue after MD simulation
0
gravatar for sakshisingh.bioinfo
21 months ago by
India/Varanasi/BHU
sakshisingh.bioinfo30 wrote:

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

ADD COMMENTlink modified 10 months ago by rprog00830 • written 21 months ago by sakshisingh.bioinfo30
0
gravatar for rprog008
10 months ago by
rprog00830
rprog00830 wrote:

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

ADD COMMENTlink modified 10 months ago • written 10 months ago by rprog00830
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1725 users visited in the last hour