AMBER Archive (2006)

Subject: AMBER: Announcement: Parameters for Modified Nucleosides in RNA

From: Raviprasad Aduri (
Date: Mon Oct 09 2006 - 16:13:56 CDT

Dear All,

I am very glad to inform you all that we (Prof. SantaLucia's Lab in
collaboration with Prof.Schlegel's Lab at Wayne state University, Detroit)
successfully developed AMBER force field parameters for all the 103
naturally occurring modified nucleosides in RNA. We made a database for
these parameters to be available to the research community. One can access
these parameters by going to the following website

The 'PDB', 'prepin' and 'frcmod' files for each modification are given in
the website. If you double click the desired modification, you can download
all these three files in one zip file and also can download the RESP
input,output files along with the optimized geometries and electrostatic
potential point (*.dat file) files.

The manuscript for this work is being submitted and will be made available
shortly on the web page.

If you have any questions, comments, or suggestions please feel free to
contact me ( or Prof.SantaLucia (

Raviprasad Aduri
Graduate Student
Prof.SantaLucia's Lab
480 Chemistry
Wayne State University
Detroit MI 48202

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