Dear Moitrayee,
> 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.
I would simply check that the structure obtained after geometry
optimization is 'similar' to the experimental one. If not, a variation
of the whole molecule approach (described in the previous email) could
be to use dihedral constraint(s) (a minimum number of constraints) to
match the experimental conformation.
You could use R.E.D. Server to perform geometry optimization with
dihedral constraints from a P2N file;
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#CONSTRAINT
If you do so, please select Gaussian version 2003 because the format
of constraints has changed in Gaussian 09 C.01.
regards, Francois
>>> 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 Thu Jan 17 2013 - 00:30:02 PST
