AMBER Archive (2006)

Subject: Re: AMBER: nmode: number of atoms limitation

From: David A. Case (case_at_scripps.edu)
Date: Tue Aug 29 2006 - 00:55:53 CDT

On Tue, Aug 29, 2006, AYTUG TUNCEL wrote:
>
> I am trying to do nmode calculation of mm_pbsa method using amber8. My
> protein is dimeric composed of totally 13776 atoms (both chains have nearly
> equal length). I am wondering about the maximum number of atoms that nmode
> can be applied. As far as I found in the archive it is about 8000 atoms. If
> this is the case how can I apply the method to my system, is there any
> trick about changing a parameter? thanks in advance...

This size would require a *lot* of patience and computer memory, and is
probably not realistically feasible with Amber's nmode program.

You might consider looking at NAB:

     http://www3.interscience.wiley.com/cgi-bin/abstract/112750181/ABSTRACT
     http://www.scripps.edu/case

But this is a real daunting project. You might really want to consider other
methods of estimating entropies, (or even of investigating protein-protein
interactions, depending on what your goals are.)

...dac

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