Dear Francois,
Thanks for the reminder! I am also interested in generating parameters for
more unusual moieties, such as the 2'3' cyclic phosphate product of
ribozyme cleavage, and was thinking that perhaps the RED server doesn't
tolerate such structures? If I am mistaken, however, I might try the RED
server again.
Thank you so much, and have a great day,
Kamali
On Sun, Oct 13, 2013 at 10:05 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Kamali,
>
> if you have an open valency in your molecular system and/or want to
> generate a molecular fragment you might try R.E.D. Server at
> q4md-forcefieldtools.org
>
> regards, Francois
>
>
> > 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.
>
>
>
> > 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 - 08:00:02 PDT
