Dear Ambers users and developers,
I have to derive atomic charges for Ibuprofen, which has two enantiomeric
forms.
I should study the diffusion of anionic ibuprofen in a negatively charged
matrix.
I have already had a look at the past messages in the mailing list, as well
as in the RED website (where is topic is discussed) but I still have not a
clear idea about how to proceed.
For the sake of completeness: I have the crystal structure of ibuprofen and
I am familiar with Gaussian and RESP procedure.
As far as I could understand, the set of atomic charges for two enantiomers
should be the same, in order to properly compare, e.g., binding affinities.
My question is: is there an optimal, or suggested, charge derivation
protocol?
In principle, I could compute through RESP the charges for one enantiomer,
and "copy" the same set for its mirrored image. This would "honor the MM
model", according to the f.a.q on RED website. I could also perform a
multiconformational fit using both structures.
I tried to compute a set of charge for each enantiomer. The sets of charges
have some discrepancies (they are not very dramatic, but there are) because
according to DFT optimization at B3LYP/6-31g(d,p) level of theory they are
not exactly mirrored. Maybe I should try an higher level of theory (MP2 or
so).
Since I am a little bit confused, I would like to ask if you have some
suggestions.
Thanks in advance for your help,
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jul 11 2015 - 03:00:02 PDT
