AMBER Archive (2009)

Subject: [AMBER] Creating conditions for biased MD

From: Francesco Pietra (
Date: Mon Mar 30 2009 - 05:16:54 CDT

I would like to modify the conformation of a protein at one helix,
which is bent at a region of three amino acids, Ile, Gly, Gly. Viewed
in cartoon representation, it is constituted of two straight portions
interconnected through a largely non helical set of the three amino

I would appreciate suggestions how to get the three aa taking part to
the well ordered helical conformation, so that what is now (in
cartoon) two straight portions interconnected by something like a loop
becomes a wholly straitened motif. Rotation about dihedrals? Make the
process with the isolated helix or in the whole context of the

I guess that steered MD (on which I have no experience) is the
approach in Amber, though I wonder how to provide the target.
Possibly, any biased MD should be carried out in explicit medium. In
my hands, continuum models were unsuccessful with this protein.

If these are not such naive questions to merit attention, thanks

francesco pietra

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