Dear Francois,
Thanks for your prompt and patient reply.As a beginner for MD, i
benefit a lot from you.
Now, i think i should use amber force field for FAD because i found
many papers and datas show they use this method.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.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.
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?
Thank you very much!
Best regards,
Xiangqian kong
FyD <fyd.q4md-forcefieldtools.org> at Mon, 23 Aug 2010 09:28:37 wrote:
>Dear Xiangqian Kong,
>
>> Recently£¬i am working to develop the RESP charge for co-factor FAD.
>> then i have some naive questions list blow about the RESP charge
>> and parameters drived for FAD .
>>
>> 1) I notice that the atom styles someone used in their papers for
>> FAD belong to the AMBER Force Field rather than GAFF.But the FAD is
>> organic small molecular, i don't know which force field should i use
>> for FAD and what influences it will bring to the final simulation
>> if i use GAFF force field¡£
>
>Why using GAFF for FAD ? http://en.wikipedia.org/wiki/FAD
>There is a nucleotide fragment; right ? So what about using parm99 or
>any adaptation ?
>
>> 2) I use the Gaussian 03 software(# opt hf/6-31g(d)
>> geom=connectivity pop=mk iop(6/33=2,6/42=6)) to calculate the ESP
>> ,and then fit the charge with antechamber(antechamber -i s.oug -fi
>> gout -o s.prep -fo prepi -c resp ),but i found my result was
>> inconsitent with someone who used the RESP software.So, i don't know
>> whether i should cite their result or just use my result .what are
>> the reasons for our differences?
>
>- Charge derivation is error-prone.
>- Many parameters affect charge values.
>- Every program has its own specificities. For instance,
>iop(6/33=2,6/42=6) are not the original parameters used by Kollman &
>co-workers.
>See http://www.ncbi.nlm.nih.gov/pubmed/20574571
>
>If you want to derive reproducible charge values, I would like to
>suggest you to use the R.E.D. Tools/R.E.DD.B. where all the parameters
>used in charge derivation have been rigorously studied. If you decide
>to use the R.E.D. Tools your charge values will be reproducible (and
>obviously the charges you will try to reproduce will not be
>reproducible if not previously derived with R.E.D./R.E.DD.B.).
>
>We do have RESP charge values for FAD and more; I can send you these
>parameters (used with parm99) if you want.
>
>regards, Francois
>
>
>
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>http://lists.ambermd.org/mailman/listinfo/amber
>
Best regards,
Xiangqian Kong
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Received on Mon Aug 23 2010 - 08:30:05 PDT
