Re: [AMBER] Production md

From: case <>
Date: Mon, 13 Aug 2012 08:35:01 -0400

On Mon, Aug 13, 2012, ariana karakutuk wrote:

> I'm new in AMBER. I'm trying to fold the missing sequences of a protein,
> but in the result the molecules diffuse very far away from each
> other. Here's my input file:

Please describe your calculation in more detail. It looks like maybe(??)
you have (experimental?) coordinates for residues 1-8 and 27-105, but not for
residues 9-26. But you don't say how you prepared the initial coordinates,
nor what the "molecules" are that diffuse far away from each other. It's hard
to give any good advice without more idea of what you did.

[Note: if you do have a big stretch of missing residues in a single
polypeptide chain, Amber is not a very good program to estimate where the
missing pieces are. In this case, you would probably want a homology modeling
program of some sort.]


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Received on Mon Aug 13 2012 - 06:00:06 PDT
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