I suppose you should use -nc option (net charge) of antechamber if
parametrized molecule has non-zero charge.
On Fri, Nov 25, 2011 at 5:17 PM, <fn1.rice.edu> wrote:
> Hi,
>
> I want to generate the parameter with Antechamber for
> 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE, where the pdb 1st0
> contains this ligand. The question
> is that this ligand has 7-methyl group on its nitrogen, which makes it
> have a one
> positive formal charge. However, Antechamber could not detect the
> charge here and
> regard the whole ligand as a neutral one.
>
> Could anyone please give some suggestions on this?
>
> Thank you very much!
> Regards,
> Fengyun
>
>
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--
Dmitry Nilov
Faculty of Bioengineering and Bioinformatics,
Lomonosov Moscow State University
web: http://enzyme.fbb.msu.ru/
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Received on Fri Nov 25 2011 - 07:00:03 PST
