Thanks Dr. Justin for your reply On Fri, Mar 31, 2017 at 6:11 AM, Justin Lemkul <jalem...@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 <zebami...@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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.