AMBER Archive (2004)

Subject: AMBER: parameter development for nucleotide analogues

From: Vlad Cojocaru (
Date: Wed Jul 07 2004 - 05:37:50 CDT

Dear amber users,
  I have developed new parameters for several fluorescent base analogues
for incorporating them into RNA. I would like to publish the results and
I was wondering how could one prove that the parameters are performing
well. From your own experience could you indicate me what kind of
calculations could one perform in order to show that these parameters
perform well. They were developed by analogy with gaff force field and
the charges were calculated with RESP as described for Amber (Gaussian +
RSEP) using a methyl group instead of sugar.
  Thank you very much for any kind of suggestions
BEst wishes

Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
home tel: ++49-551-9963204  

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