Dear Xiangqian Kong,
> Now, i think i should use amber force field for FAD because i found
> many papers and datas show they use this method.
This is simply a question of choice. Personally, I only use GAFF as a
source of obvious FF parameters such as for an aromatic counter part,
and always recompute key dihedral FF parameters or use these from
99SB/parm99/98.dat/GLYCAM.
> But i am still
> confused about the reasons to use Amber Force field rather than gaff
> because there is a flavin ring that belongs neither amino acid nor
> nuclotides.
The key point here is what part you think is important for the
conformation of FAD, FADH2 etc... ? the nucleotide/phosphate parts or
the aromatic part ? I would vote for the 1st one ;-) thus I would use
parm99.dat and its different modifications. But once again this is a
question of choice and FF adaptation.
> what's more, I also don't know whether the difference of
> force field used for FAD will cause some bad influnces on our simulation.
This is always a good idea recomputing important dihedral FF
parameters instead of trusting what is available in a generic FF.
> In the mean time,i would like to have the resp charge and parameters
> of FAD if you can kindly E-Mail them to me.And it's reasonable if i use
> them in FF99SB?
ok
Personally, I would use FF99SB with FAD/FADH2/analogs checking key dihedrals.
regards, Francois
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Received on Mon Aug 23 2010 - 12:30:05 PDT
