Thank you very much, Dr. Case; I wasn't aware that the "-nc" flag was only
for amb1-bcc calculations. Would you be able to tell me what the warning
means? It seems to me that antechamber is misinterpreting the fact that the
N1 atom now only has 2 bonds as an indication of incomplete valence, but
I'm not sure how much this will distort the resulting charges, and also if
there's a way to let antechamber know that the "incomplete valency" is
intentional.
Thanks everybody, and have a great day,
Kamali
On Sat, Oct 12, 2013 at 11:39 AM, David Case <dacase.rci.rutgers.edu> wrote:
>
>
> > On Oct 12, 2013, at 10:22 AM, Kamali Sripathi <ksripath.umich.edu>
> wrote:
> >
> >
> > I am using Gaussian and antechamber to parameterize an N1-unprotonated
> > guanine for RNA. I initially generated a prepc file while forgetting to
> add
> > the "-nc -1" flag. I re-ran the calculations using this flag, but the two
> > resulting prepc files are the same. I have compared prepc files for other
> > molecules with and without the "-nc" flag and found the same thing
> happen.
>
> The -nc flag only applies to am1-bcc charge calculations. You provided
> the net charge to Gaussian in its inout file.
>
> ...dac
>
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Received on Sun Oct 13 2013 - 06:30:02 PDT
