[AMBER] Protein Stability in amber mmpbsa tutorial

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From: MUHAMMAD IMTIA SHAFIQ <imtiazshafiq.gmail.com>
Date: Mon, 22 Feb 2010 20:54:54 +0000

Dear All,

I would like to know can we view a protein stability in VMD after the heat, density or equilibrium simulations in mmpbsa run? I have tried visualisation of .mdrcd files in VMD downloaded from the amber mmpbsa tutorial page and found some residues are badly distorted however, overall protein seems to be intact.

Does these distorted amino acids effect protein stability or it is just a visualisation issue ?

Regards
Imtiaz
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Received on Mon Feb 22 2010 - 13:00:04 PST