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 Tue Apr 29 2014 - 13:00:03 PDT
