Re: Avoiding alpha-helix distortions

From: Eric H. Lee (
Date: Wed Jul 02 2008 - 10:41:01 CDT

I agree with Peter. Something else to check for is whether the
crystal structure contains an artificial constraint like heavy metal
ions which may coordinate various parts of your protein together.
Whether you end up modeling these ions (or even seemingly innocuous
elements such as crystal waters) as part of your simulation makes a


On Jul 2, 2008, at 7:59 AM, Peter Freddolino wrote:

> If you're willing to grab the cvs version of namd, you can use the
> extrabonds feature (discussed previously:
> 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

Eric H. Lee
Medical Scholars Program
Theoretical and Computational Biophysics Group, UIUC

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