Re: [AMBER] Charge calculation methods for RED server

From: Ken Merz <kmerz1.gmail.com>
Date: Wed, 8 Jan 2014 13:08:32 -0500

Hi,

The RED server is for RESP charge evaluation and I am not sure if it can help design metal ion FFs and if so, how good it is overall for these cases. Ambertools has metal ion FF building capabilities (MCPB) including charge derivation. The reference doi describing this is attached. Good luck!

Kennie

10.1021/ct1002626


On Jan 8, 2014, at 4:56 AM, Yip Yew Mun <yipy0005.gmail.com> wrote:

> Hi, I'm not sure if this is the right place to ask about the R.E.D server, so I'm just going to give it a shot.
>
> I'm planning to simulate a zinc finger where the zinc ion is coordinated to 4 other Cys residues. I plan to calculate the charge of the Zn ion since coordination would definitely have changed its +2 charge. I know I can rely on the RED server for this, but under the charge method (e.g. Resp-A1A), how do I know which one is suitable.?
>
> Also, while the RED website has a tutorial for metal inorganic complexes, is there a step by step guide as well on using the RED server for deriving charges of metals in proteins.?
>
> Much appreciated for any help offered. =)
>
> Yew Mun
>
> Sent from my iPhone
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Kenneth M. Merz, Jr.
Director, Institute for Cyber Enabled Research (iCER)
Joseph Zichis Chair in Chemistry
Department of Chemistry
Department of Biochemistry and Molecular Biology
Michigan State University
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East Lansing, MI 48824-1322

Phone: 517-355-9715 (Chemistry)
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e-mail: kmerz1.gmail.com
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However, one should bear in mind that a macromolecular refinement against high resolution data is never finished, only abandoned.

George Sheldrick (2008), Acta Crystallogr. D64 112122.

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Received on Wed Jan 08 2014 - 10:30:02 PST
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