Dear Francois,
Thanks a lot for your email.
We do have an electron density in the crystal structure to which the citrate was
modeled. But I am not sure what sort of experimental data you are referring to.
It would be immensely helpful if you please elaborate a little more so that I
can speak to my experimental collaborator on this issue.
Thanks again and would look forward to hear from you.
Best Regards,
Moitrayee
> Dear Moitrayee,
>
>> I am performing a MD for which I would require citrate ion (-3)
>> parameters. It
>> would great if someone could help me with finding if there are
>> published citrate
>> ion parameters. I have searched the AMBER archive but did not get them.
>
> Citrate is a complex case; this is small molecule with 3 negative charges...
>
> If you decide to derive charges for the whole molecule, the
> conformation obtained after geometry optimization is unlikely to be
> representative of what you want...
>
> If you decide to follow the building block approach (see
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#17) the
> constraints used during charge derivation are likely to strongly
> affect the fit...
>
> Do you have experimental data about citrate that could be used to
> guide the charge derivation procedure?
>
> regards, Francois
>
>
>
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Received on Wed Jan 16 2013 - 01:30:02 PST
