AMBER Archive (2009)

Subject: Re: [AMBER] Creating conditions for biased MD

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Mar 30 2009 - 06:56:36 CDT

francesco, I think dihedral restraints may be the only way to go without a
helical ref structure. you'd definitely want to also restrain all other
residues in this helix to maintain it, or else you might just move the bend.
when changing the restraints over time, give thought to which direction to
rotate, which depends on the initial conformation of the Gly residues, if
they are currently adopting positive phi values then it's more complex than
just going from pp2 to alpha, for example, where you can just reduce psi.

On Mon, Mar 30, 2009 at 6:16 AM, Francesco Pietra <chiendarret_at_gmail.com>wrote:

> Hi:
> 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
> acids.
>
> 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
> protein?
>
> 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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