Dear Francois,
Thanks for your patient reply.
I agree with your point that the nucleotide/phosphate parts is important
for the conformation of FAD and it's analog.Meanwhile, i think it's
reasonable to use GAFF for aromatic counter part and recompute or use
these key dihedral FF parameters from 99SB/parm99/98.dat/GLYCAM.
I would like to have your resp charge and FF parameters for FAD if
you can kindly e-mail them to me.Meanwhile, how should I cite your RESP charges and FF parameters and acknowledge you?
Waiting for your reply.
Best regards,
Xiangqian Kong
FyD <fyd.q4md-forcefieldtools.org> at Mon, 23 Aug 2010 21:22:06 wrote:
>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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>
Best regards,
Xiangqian Kong
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Received on Mon Aug 23 2010 - 19:00:03 PDT
