Question: stereochemical issue after MD simulation
0
gravatar for sakshisingh.bioinfo
15 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 4 months ago by rprog00830 • written 15 months ago by sakshisingh.bioinfo30
0
gravatar for rprog008
4 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 4 months ago • written 4 months ago by rprog00830
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