[AMBER] What to expect when MD a peptide and a small organic molecule ?

From: Jean-Patrick Francoia <jeanpatrick.francoia.gmail.com>
Date: Wed, 4 Nov 2015 14:42:22 +0100


I'm trying to do MD on a system made of a short peptide and the molecule
of cocaine. It is just a training. The peptide is a hexapeptide
(QHWWDW), easily generated with the 'sequence' command of xleap. The
library for the cocaine residue was built using antechamber.

I merged the peptide and the cocaine. I performed a short minimization
using implicit solvent, and then, I tried to run a molecular dynamic. It
"worked", meaning the MD completed without errors. I now have a splendid
trajectory (1 ns). But I don't know what it means, and what to expect.

I know the peptide and the cocaine bind "strongly" (I can't quantify
strongly). There are experimental evidences. So I was expecting the
peptide would fold and catch the cocaine, and that at some point, the
complex would stop changing. I was hoping to see a particular
conformation of the complex. Instead, I see the two molecules
interacting, but no preferred conformation (ok, maybe one, appearing
sometimes), but nothing really fixed.

Was I right to expect that, or not ?


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Received on Wed Nov 04 2015 - 06:00:05 PST
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