I did a simulation of the solvated ring and there wasn't big
distortions in the planarity. I'll also check in gas phase, just in case.
Thank you so much for your kind help and advices.
Best Regards,
Leandro Bortot
2013/2/8 David A Case <case.biomaps.rutgers.edu>
> On Fri, Feb 08, 2013, Leandro Bortot wrote:
> >
> > I'm using AmberTools 12. Here antechamber also works fine and it is
> > even possible to get the parameters from parmchk.
> >
> > What I'm worried about, though, is with the output of acdoctor -i
> > threer.mol2 -f mol2:
> > Error: weird atomic valence (5) for atom (ID: 11, Name: C3), please check
> > atomic connectivity
>
> You should always take care with automatically-generated force field
> parameters, but yes, I think you can probably ignore the acdoctor warnings.
>
> I'd certainly suggest running simulations of the ligand by itself, even in
> the
> gas phase, to sure that it doesn't want to adopt weird geometries that you
> are
> unhappy with. Such calculations would take only short time. If the
> molecule
> stays planar and fairly rigid, you are probably fine.
>
> ...good luck...dac
>
>
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Received on Fri Feb 08 2013 - 13:00:04 PST
