Re: Calcium ion-Protein Binding

From: JC Gumbart (
Date: Mon Sep 22 2008 - 13:42:28 CDT

Can you send me your psf and pdb file off list? It sounds like
something really unusual is going on here.

On Sep 22, 2008, at 1:33 PM, MIke S wrote:

> I should add that even if I created bonds to the calcium ions, I
> don't think it would keep the calcium's in place. I noticed that
> for one of my structures each calcium is bonded to a single residue
> through hydrogen and when I run an equilibration the bond is
> stretched dramatically due to the displacement of the calcium ion.
> So, adding additional bonds to the calcium ion (there should be
> roughly six bonds surrounding each calcium) would probably not
> restrain the atom in the binding site.
> On Mon, Sep 22, 2008 at 1:54 PM, MIke S <> wrote:
> 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,
> Mike
> 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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