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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Received on Mon Aug 23 2010 - 00:30:03 PDT
