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 - 12:30:03 PST
