Re: [AMBER] Charge calculation methods for RED server

From: Ken Merz <kmerz1.gmail.com>
Date: Thu, 9 Jan 2014 15:18:36 -0500

Hi,
 Sorry to of offended, but my sentence was suitably qualified! Take care,
Kennie


On Jan 9, 2014, at 3:12 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:

> Dear Kennie,
>
>> 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.
>
> I think this statement is simply not correct; R.E.D. Server is not
> only for RESP charge derivation; and for your information R.E.D.
> Server Dev. handles all the elements of the periodic table and
> performs far more than charge derivation...
>
> See http://q4md-forcefieldtools.org/REDS-Development/news.php
> vs http://q4md-forcefieldtools.org/REDS/news.php
>
> regards, Francois
>
>
>> 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
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> 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
>> 578 S. Shaw Lane
>> East Lansing, MI 48824-1322
>>
>> Phone: 517-355-9715 (Chemistry)
>> 517-884-2540 (iCER)
>> 517-353-7248 (Fax)
>> Cell: 814-360-0376
>>
>> e-mail: kmerz1.gmail.com
>> http://www.merzgroup.org/
>> https://icer.msu.edu
>> iCER Help: https://contact.icer.msu.edu/contact
>>
>> 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 112-122.
>
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber

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
578 S. Shaw Lane
East Lansing, MI 48824-1322

Phone: 517-355-9715 (Chemistry)
                    517-884-2540 (iCER)
                517-353-7248 (Fax)
Cell: 814-360-0376

e-mail: kmerz1.gmail.com
http://www.merzgroup.org/
https://icer.msu.edu
iCER Help: https://contact.icer.msu.edu/contact

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 Thu Jan 09 2014 - 12:30:04 PST
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