RE: Calcium ion binding protein

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
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: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of vsweta_at_iastate.edu
Sent: Tuesday, October 21, 2008 4:28 PM
To: namd-l_at_ks.uiuc.edu
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,

http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/8348.html

I understand I need to apply constraints to the calcium ions but I am unable
to
figure out how to go about it.I have two segments one containing the protein
and
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
Sweta

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