Re: [AMBER] MD study of transition of protein from one conformation to another

From: David A Case <david.case.rutgers.edu>
Date: Mon, 28 Dec 2015 15:42:40 -0500

On Mon, Dec 28, 2015, Abhilash J wrote:
>
> I have a protein which exists in two conformations. I have PDB files
> (from RSCB PDB ) of both the conformations. I need to run a MD which starts
> from one conformation and moves towards the other conformation (kind of
> guided MD). I fear normal MD will either take too long if left unguided or
> even not give any result.

This is called "targeted MD": please see section 21.3 of the Amber 2015
Reference Manual.

....dac 

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David A. Case                         | david.case.rutgers.edu
Dept. of Chemistry & Chemical Biology |
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Received on Mon Dec 28 2015 - 13:00:03 PST
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