Re: Avoiding alpha-helix distortions

From: Eric H. Lee (
Date: Sat Jul 05 2008 - 12:22:24 CDT

It would be worthwhile to run two sets of simulations - one with the
sulphate ion, and one wtihout, to see whether the sulphate
artificially constrains the protein into a particular helical
conformation (it almost certain does, but then I've not seen your


On Jul 5, 2008, at 12:38 AM, Praveen Agrawal wrote:

> Eric, I have a further query on the ion modeling with Protein. I am
> dealing with a protein which has sulphate ion and the crystallization
> paper says that the sulphates were added to make the protein
> 'amenable' to crystallization process. So, does this mean that while
> doing MD, I should take 'this' sulphate explicitly?
> Regards,
> Praveen
> On Wed, Jul 2, 2008 at 9:11 PM, Eric H. Lee <>
> wrote:
>> 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 difference.
>> -Eric
>> 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

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

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