[gmx-users] FAD parameters in CHRAMm36 ff

[Amir Zeb]

Thanks Dr. Justin for your reply

On Fri, Mar 31, 2017 at 6:11 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/31/17 3:54 AM, Vytautas Rakeviius wrote:
>
>> I think you should use cgenff for FAD in such case. They are compatible
>> and can by used together.
>>
>>
> Indeed, though one should pay close attention to the parameter penalties
> in the adenine nucleotide portion of the molecule, as that part is covered
> by standard CHARMM.  Any deviations should be investigated, though they
> will probably be small and therefore unimportant.  Most of the necessary
> functional groups for FAD are already in CHARMM, just not parametrized
> explicitly, so I suspect a CGenFF topology to be of pretty high quality
> since the analogy will be strong.
>
> -Justin
>
>
>
>>     On Friday, March 31, 2017 9:29 AM, Amir Zeb <zebamir85 at gmail.com>
>> wrote:
>>
>>
>>  Hello Folks,
>>
>> I want to simulate a protein where FAD is included as co-factor. I will
>> use
>> CHARMm36 ff but I don't know the residue ID for FAD in this particular
>> forcefield. Anyone please let me know by which name FAD is represented in
>> CHARMm36 ff?
>>
>> Thanks in advance!
>>
>> ~Amir
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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