Re: Avoiding alpha-helix distortions

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Jul 02 2008 - 07:59:15 CDT

If you're willing to grab the cvs version of namd, you can use the
extrabonds feature (discussed previously:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/6203.html) to
constrain the backbone dihedrals of the helix. You have to set up the
extrabonds file, but this shouldn't take more than a simple script in
vmd. Constraining the backbone hydrogen bonds, the dihedrals, or both
all seem to work in my experience. However, you may want to try to
understand more clearly *why* the helices are distorting, before you
apply external forces to prevent it. If the force field is saying they
should distort, there must be some reason -- one should be careful in
defining what is "correct" for secondary structures if they're in an
environment that seems to destabilize what you expect.

Best,
Peter

Valeria Losasso wrote:
>
> Hi all,
> my question is the following: in my protein I have three long
> interacting alpha helices. First of all I minimized the side chains by
> blocking the backbone through a constant force. Nevertheless, if I try
> to minimize the entire protein (since the previous step is clearly not
> enough to start a dynamics) I get a series of distortions in the
> backbone of the helices, probably due to their length and position.
> The point is: is there an "automated" way to keep the secondary
> structure with the correct parameters (dihedral angles and so on) - I
> mean: a way to say "I want a standard alpha helix from residue X to
> residue Y"?
> Or I have to setup manually all needed restraints among all atoms
> involved? And in this second case, is it more convenient to restraint
> the hydrogen bonds length or dihedral values or what?
>
> Best regards,
> Valeria Losasso

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