[gmx-users] FAD parameters in CHRAMm36 ff

[Justin Lemkul]

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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