Re: [AMBER] How to generate boron atom paramaters?

From: Ken Merz <kmerz1.gmail.com>
Date: Fri, 10 Jan 2014 16:52:34 -0500

Hi,
 OK. That's not as hard as a carborane, for example. There are several ways you could get what you need I believe. Good luck.
Kennie

On Jan 10, 2014, at 4:40 PM, Mengyuan Zhu <mzhu6.student.gsu.edu> wrote:

> Thank you!
>
> It's boronic acid. I am going to study MTK++.
>
> Sent from Windows Mail
>
> From: Ken Merz<mailto:kmerz1.gmail.com>
> Sent: ?Friday?, ?January? ?10?, ?2014 ?3?:?58? ?PM
> To: amber.ambermd.org<mailto:amber.ambermd.org>
>
> Hi,
>
> Can you be more specific about your needs? Are you dealing with say a boronic acid/ester or are you dealing with a boron cage or carborane? If it is a boronic acid/ester then a program like MCPB (among others) can give you charges and force constants, while a carborane might also work fine in MCPB, but would be tricky due to the interesting structural details. What to use for LJ values for boron is something I am not expert on, but perhaps some digging in the literature would yield some appropriate values. In the end validation that you are reproducing boron chemistry with your FF will be key. Good luck!
>
> Kennie
>
>
>
> On Jan 10, 2014, at 3:32 PM, Mengyuan Zhu <mzhu6.student.gsu.edu> wrote:
>
>> Thank you. I will have a try...
>>
>> Sent from Windows Mail
>>
>> From: David A Case<mailto:case.biomaps.rutgers.edu>
>> Sent: ?Friday?, ?January? ?10?, ?2014 ?3?:?10? ?PM
>> To: amber.ambermd.org<mailto:amber.ambermd.org>
>>
>> On Fri, Jan 10, 2014, Mengyuan Zhu wrote:
>>>
>>>
>>> As my molecule has boron atoms, antechamber can not deal with it. How
>>> can I do? I have generated Gaussian output file with HF/6-31G*basis
>>> set. Thank you!
>>
>> Maybe someone else will pipe in here, but as far as I know, there is no
>> support for boron compounds in Amber. You'll have to do some literature work
>> to see how feasible it is (depends a lot on the nature of your compound!)
>> to generate MM parameters. [My memory(!) of boron chemistry is that it is
>> distinctly odd, with lots of bonds that don't fit the usual 2-electron-bond
>> picture....]
>>
>> ...good luck...dac
>>
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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
> 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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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 Fri Jan 10 2014 - 14:00:03 PST
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