On Thu, Aug 16, 2018, Sergey Samsonov wrote:
>
> I'm trying to get gaff parameters for a molecule of berenil following the
> standard procedure from the antechamber tutorial. When I use bcc charge
> model, the atomic types as well as the charges are recognized wrongly (see
> am1bcc_berenil.mol2 attached): among other inconsistencies, one of the ring
> is treated as a benzene ring, which is correct and another is not.
This is certainly an interesting and unusual molecule. It is far enough
away (I think) from molecules that were used in the development of GAFF
that some weird behavior is not unexpected.
It seems arguable to me that the two "benzene" rings are in fact in
different environments. But it's easy enough to fix the atom types by
hand, if you are convinced you know what they should be. One suggestion
would be to minimize the structure in DFT or MP2, and look at the
resulting bond lengths. That should provide a clue about what the best
atom typing should be.
If you are concerned about charges, be sure to check the resp charges
for this molecule: resp charges don't depend on any atom typing, and are
probably more reliable for rather unusual chemical species like this
one.
...hope this helps....dac
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Received on Thu Aug 16 2018 - 09:00:03 PDT
