Re: AMBER: Modified RNA Bases

From: FyD <>
Date: Tue, 27 Sep 2005 07:45:17 +0200

Quoting Raviprasad Aduri <>:

> 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.

You can also use Tripos .mol2 file. See

In this case, you have to build the 'nucleoside.mol2' file (this is done
automatically in R.E.D.-III)


The Cart. coord in this .mol2 does not have to be 'perfect': They can be
'bizarre' ;-) since only the topology matters...
You can build a Tripos file from a PDB file for instance using babel...

regards, Francois

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Received on Tue Sep 27 2005 - 06:53:00 PDT
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