Re: Avoiding alpha-helix distortions

From: Praveen Agrawal (
Date: Sat Jul 05 2008 - 00:38:45 CDT

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?


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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:48:01 CST