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.
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. I could also perform a
multiconformational fit using both structures.
Since I am a little bit confused, I would like to ask if you have some
suggestions.
Thanks in advance for your help,
Tommaso Casalini
Postdoctoral fellow.ETH Zuerich
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Received on Fri Jul 10 2015 - 14:00:03 PDT
