RE: Calcium ion binding protein

From: JC Gumbart (
Date: Wed Oct 22 2008 - 09:40:47 CDT

No, you don't need to use covalent bonds. In the case you linked to, there
was an issue with the charges used.

-----Original Message-----
From: [] On Behalf
Sent: Tuesday, October 21, 2008 4:28 PM
Subject: namd-l: Calcium ion binding protein

Hi all
I am trying to simulate a calcium ion binding protein using NAMD. From a
previously posted thread,

I understand I need to apply constraints to the calcium ions but I am unable
figure out how to go about it.I have two segments one containing the protein
the other containing the calcium ions. How do I reflect the covalent bonds
between the ions and the protein in the topology/parameter file ?

Thanks for your attention

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