stereochemical issue after MD simulation
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
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rprog008 •
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singh.bioinfo •
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singh.bioinfo •
1 answer
At first you fix the PDB file of protein via WhatIf server and later perform MD simulation. It generally work. :)
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rprog008 •
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