peptide conformation search examples

From: Andrew D. Fant (
Date: Tue Jan 30 2007 - 14:21:49 CST

Afternoon all.
    I've got a short ( ~40 residue) peptide that I want to do some conformer
generation for. I'm still new at using namd, though. I can probably work out a
scheme for multiple simulated annealing runs without too much difficulty, but I
am a little more leery of trying to do some sort of automated analysis of the
resulting structures to ensure that they are actually distinct.
    Is there anyone out there who has done this sort of thing who is willing to
share a copy of the tcl they used to set this up? Even if it is useless for
direct submission, having an example would make getting my bearings a lot easier.

Thanks in advance,

Andrew Fant    | And when the night is cloudy    | This space to let
Molecular Geek | There is still a light          |---------------------- | That shines on me               | Disclaimer:  I don't
Boston, MA     | Shine until tomorrow, Let it be | even speak for myself

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