Re: Calcium ion-Protein Binding

From: MIke S (
Date: Mon Sep 22 2008 - 12:54:20 CDT

JC thanks for the tips.

So far I tried creating bonds between a caclium ion and the surrounding
residues by adding the corresponding bonds in the PSF file, but that hasn't
worked because I don't have the correct parameter set for the Calcium-Oxygen
bonds in the parameter file. So, I tried using the values from the OH1-CT1
bonding parameter to see if I could minimize the system, but I got a
Segmenation Fault error. I'm not sure why this happened. I looked this
error up on this forum and from my understanding this might be related to
overlapping of coordinates. I'm running an equilibration of my protein
with fixed calcium atoms right now. My main concern with this strategy is
that the simulation won't be a true representation of the unfolding that
will occur in the calcium binding domains.

I neglected to mention in my previous message that I'm running the
simulations in vacuo. Do you think this would be contributing to the
displacement of the calcium ions?

Thank you for the assistance,


On Thu, Sep 18, 2008 at 3:22 PM, JC Gumbart <> wrote:

> 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.
> 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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