AMBER: conformational sampling of a peptide

From: Hannes Barsch <>
Date: Tue, 24 May 2005 10:58:04 +0200

Dear AMBER community,

I work on the conformational sampling of a dye labelled oligo peptide. The
peptide is 9 amino acids in length, of which 8 are frozen using IBELLY. The
last amino acid and the dye bonded to the first aa are to move freely to
investigate the distance distribution over time. Energies are of no
interest - the sampling is just a coarse study.
After having run ordinary MD simulations I found out that the dye is stuck
in an energetic minimum and hardly moves. Therefore, I have changed the
force field parameters of the atoms linking dye and peptide: all torsional
potentials were set to zero as well as the bond angle potentials.
Electrostatics were switched off by raising DIELC to 1000000 in the sander
MD input file.
Still the movement of the dye moiety has not improved very much. It still
sticks to the peptide backbone. I guess this might be due to the nonbounded
interaction. How can I switch these interactions off? I already tried to
reduce CUT in the sander input file but I can do so only down to just above
8.0 A. Is there a better or may be an easier way to work with a pseudo hard
sphere model in AMBER?
Thanks for any hints!


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Received on Tue May 24 2005 - 10:53:00 PDT
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