Hi Kamali,
I guess you can take parameters from SI
in JOURNAL OF PHYSICAL CHEMISTRY B, 114, 2010, 8701.
p. 4 in SI
Jiri
On Sat, 12 Oct 2013, Kamali Sripathi wrote:
> Date: Sat, 12 Oct 2013 10:22:10 -0400
> From: Kamali Sripathi <ksripath.umich.edu>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: [AMBER] Questions regarding AMBER
>
> Dear AMBER Mailing list,
>
> 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.
>
> More importantly, I get the following warning whether or not the "-nc -1"
> flag is present:
>
> *Warning: ATOM N3 has unfilled valence, assuming the linked atom name (in
> other residue) is "M"*
> * change "M" to "-M" if ATOM N3 is linked to the immediate previous
> residue*
> * change "M" to "+M" if ATOM N3 is linked to the immediate after
> residue*
>
> Does anyone have any idea as to why the "-nc" flag appears to make no
> difference, and what this warning means? I tried looking for this warning
> in the AMBER mailing list archives and couldn't find anything, but please
> do point me to any previous messages or other resources that I might have
> missed.
>
> Thank you all, and have a great weekend,
>
> Kamali Sripathi
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Oct 12 2013 - 08:00:03 PDT
