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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Received on Wed Aug 30 2006 - 06:07:14 PDT
