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 Tue Jan 15 2013 - 23:00:03 PST
