AMBER: Modified RNA Bases

From: Raviprasad Aduri <>
Date: Mon, 26 Sep 2005 22:41:12 -0400

Dear Amber and RED users,
I am trying to develop parameters for a modified RNA base. I did the
Gaussian calculations on the base with a methyl group attached in place of
the Sugar moiety. I did the multi-orientation fit using RED II and then
used the sugar charge constraint on the methyl group in the RESP fitting.
Now my question is how do I make the "prepin" file and the "frcmod" file
for the whole nucleoside. I tried stripping the methyl group and pasting
the sugar part (from AMBER regular bases database) in the prepin file
(generated from the Gaussian output file which has the methyl group instead
of sugar) but it doesn't seem to work. Any suggestions will be greatly

Thank you for spending your valuable time to answer my question.

Best regards
Raviprasad Aduri

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Received on Tue Sep 27 2005 - 03:53:01 PDT
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