AMBER Archive (2006)

Subject: Re: AMBER: Simulating proteins with calcium ion

From: Qing Zhang (qingzhang_nyu_at_yahoo.com)
Date: Sat Dec 23 2006 - 01:26:11 CST

> ----- Original Message ----
> From: ÕÅÓÂ <clarkzhy_at_mail.bnu.edu.cn>
> In my EF-PROTEIN system, the Ca2+ coordination hold a good octahedron coordination
> if we regard the water molecule as a ligand when using the calcium parameter in
> amber99 forcefield.

I don't understand what you mean "regard the water molecule as a ligand". Is there any water molecule involving in the Ca2+ coordination?

> of cource, I change both the radius and the epsilon values to use the small
> parameter, calcium ions escape from a C2-domain, but is ok in EF-protein, while
> the Ca-O distance is too samll, only 2.1-2.4.

If I understand correctly, using the Aqvist's vdw parameters for Ca2+ causes the ions escape from one protein (with a C2-domain) but not from the other one (EF-protein)? The latter one has Ca-O distances ranging from 2.1 to 2.4 Angstrom after MD. Could you explain why the Ca2+ ions escape from the C2-domain? The shorter Ca2+ vdw radius leads to shorter Ca-oxygen distances and thus should makes the Ca-oxygen electrostatic attraction stronger.

Thanks,

Qing

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