[AMBER] Questions regarding AMBER

From: Kamali Sripathi <ksripath.umich.edu>
Date: Sat, 12 Oct 2013 10:22:10 -0400

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
* change "M" to "+M" if ATOM N3 is linked to the immediate after

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

Thank you all, and have a great weekend,

Kamali Sripathi
AMBER mailing list
Received on Sat Oct 12 2013 - 07:30:02 PDT
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