Dear Francois,
I am using angle constraints on the citrate anion (-3) based on the X-ray data.
I have attached the P2N file and the .mol2 file. After optimization, I a
conformation very similar to the experimental conformation. It would be great if
you take a quick look through them and let me know if I am making some
obvious/conceptual mistake.
Also I am using antechamber to generate the prep and frcmod file for the ion
using the following command:
antechamber -i *.mol2 -fi mol2 -o *.prep -fo prepi -nc -3 -j 5
Thanks a lot for your support.
Best Regards,
Moitrayee
> 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 Sat Jan 19 2013 - 05:30:02 PST
