Dear Francois,
Thanks for the information.
On Sun, Oct 13, 2013 at 12:44 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Kamali,
>
> See http://q4md-forcefieldtools.org/REDS-Development/popup/popkeyword.php
> vs http://q4md-forcefieldtools.org/REDS/popup/popkeyword.php
>
> "R.E.D. Server does not tolerate such structures":
> what does it mean?
>
I meant that I thought that the RED server would not be able to generate
parameters for moieties like 2'3' cyclic phosphates, but I see that I may
be mistaken.
Thank you very much, and have a great evening,
Kamali
> > 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.
>
> > 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 - 15:30:03 PDT
