Calcium ion-Protein Binding

From: MIke S (vmd.namd_at_gmail.com)
Date: Thu Sep 18 2008 - 14:13:34 CDT

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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