You have to do all that in a "post-process" mode. i.e.
write out the coordinates periodically during the MD run
and determine the properties you want either with ANAL,
MDANAL, or CARNAL depending on the information you want.
jim
On Wed, 12 Sep 2001, Elizabeth K. White wrote:
> Is it at all possible to get AMBER to output coordinates and energies for
> just a segment of the protein molecule? The NTWPRT flag seems to do some
> of this, but how to make it consider atoms 300-500, as opposed to atoms
> 1-500? More to the point, what if I want to consider, say, the dihedral
> angle energies over a certain piece of the folding protein, and ignore the
> rest? Can I ask sander to just write the energies for that piece out to
> a file? Does anyone have any helpful insights about doing this?
>
> Thanks, Elizabeth
>
>
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James W. Caldwell (voice) 415-476-8603
Department of Pharmaceutical Chemistry (fax) 415-502-1411
Mail Stop 0446 (email) caldwell_at_heimdal.ucsf.edu
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University of California
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Received on Wed Sep 12 2001 - 15:33:59 PDT
