Re: FAD topology and parameters

From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Tue Feb 18 2014 - 20:01:28 CST

To the best of my knowledge, we never made a CHARMM FAD model. You can get
an approximate topology and parameters from the CGenFF program at
paramchem.org , but because we never parameterized it, it will be *very*
approximate (especially the FAD and FADH(-) forms). When put in a
high-affinity binding pocket, it will probably stay bound and not assume
crazy conformations, but we can't say much beyond that. You could try to
refine the paramchem.org guess with FFTK ,though.

On 02/17/2014 11:15 AM, Tanner, John J. wrote:
> Thanks Flavio. I see NAD(P)(H) in toppar_c35b2_c36a2.tar, but not FAD.
>
>
>
> On Feb 17, 2014, at 6:01 AM, flavio seixas wrote:
>
>> Hi,
>> Take a look at Charmm FF release c35b2, c36a2 at http://mackerell.umaryland.edu/CHARMM_ff_params.html
>> There are topology and parameter files for NAD, NADH, FAD, FADH2
>> Regards,
>> Flavio
>>
>> -------------------------------------
>> Flavio Augusto Vicente Seixas
>> Laboratory of Structural Biochemistry
>> Department of Biochemistry
>> Universidade Estadual de Maringá, PR, Brazil
>> http://www.uem.br
>>
>> From: "Tanner, John J." <TannerJJ_at_missouri.edu>
>> To: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
>> Sent: Sunday, February 16, 2014 6:30 PM
>> Subject: namd-l: FAD topology and parameters
>>
>> Does anyone have topology and parameter files for FAD for use in NAMD?
>>
>> Thanks.
>>
>>
>> John J. Tanner
>> Professor of Biochemistry and Chemistry
>> University of Missouri-Columbia
>> 125 Chemistry Building
>> Columbia, MO 65211
>> email: tannerjj_at_missouri.edu
>> phone: 573-884-1280
>> fax: 573-882-2754
>> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
>>
>>
>>
>>
>>
>>
>
>

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