Re: Calcium ion-Protein Binding

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu Sep 18 2008 - 14:22:41 CDT

I'm a little troubled by the fact that the ions fly away. If they
are supposed to be bound, they should most likely stay bound in the
simulation. Try to look for why this happened. Could it be an
equilibration problem for example? Maybe restraining the ions and
the protein for some time first would help. Let us know what you find.

On Sep 18, 2008, at 2:13 PM, MIke S wrote:

> Hi,
>
> I would like to run NAMD on a calcium binding protein. I ran a
> simulation and noticed that the four calcium ions fly away from the
> protein. Does this mean I have to create some type of constraint
> on the calcium ions? Or is there a method to create bonds between
> the amino acids and the calcium ions to prevent this from happening?
>
> The following post might be similar to what I want to do, but I
> can't seem to make sense of the recommendations.
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/4431.html
>
> I'm thinking I'll need to make adjustments to the topology or
> parameter files, but I have not clue as to where I should start.
>
> Btw, the PDB and PSF files I'm using were generated using psfgen
> with one segment for the protein and one segment for the calcium ions.
>
> Your suggestions would be helpful.
>
> Regards,
>
> Mike

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