Jason,
Thanks for suggestion. I've solved this issue by such modification of the
charge in the ligand.lib (not mol2) file consisted of the ligand topology
which I've used during complex preparation.
James
2014-04-29 23:38 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
> On Tue, 2014-04-29 at 22:48 +0400, James Starlight wrote:
> > Dear David,
> >
> >
> > thanks for suggestions again.
> >
> > One question: what should I do with the non-integer charges (below you
> can
> > see warning obtained for my solvated system?)
> >
> > WARNING: The unperturbed charge of the unit: -2.998000 is not zero.
> >
> > In this case -2 charge came from the protein and ligand should have -1 as
> > defined during its parametrization:
> > antechamber -i ligand.pdb -fi pdb -o ligand.mol2 -fo mol2 -c bcc -s 2
> -nc -1
>
> I suggest modifying ligand.mol2 and subtracting 0.002 from one of the
> atoms with a bigger positive or negative charge.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Wed Apr 30 2014 - 00:00:03 PDT
