sander energy data

From: Raik Gruenberg <>
Date: Thu 8 Mar 2001 18:24:28 +0100 (MET)


I would like to have a look at the mden file that is advertised in the
Amber 6.0 manual to provide "extensive energy data over trajectory".
Unfortunately, regardless whether I run sander with or without the -e
option, I never get this file.

What I am eventually interested in, is to somehow map both internal and
interaction energy to structure elements. I want to identify "hot-spots"
that absorb energy during the forced unfolding of a protein. Has anyone
example ANAL scripts that deal with similar problems or should I switch to
the MM-PBSA script anyway?

Thanks a lot for any hints or comments!


Raik Gruenberg | EMBL
                                | Meyerhofstr. 1 | D-69117 Heidelberg
Tel: +49/62 21/38 72 96 | Germany
Received on Thu Mar 08 2001 - 09:24:28 PST
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