Subject: new RNA residues

From: Vlad Cojocaru <[email-masked]>
Date: Thu, 11 Apr 2002 10:28:17 +0200

Hi!
   I am trying to introduce some fluorescent base analogues 
(2aminopurine and  pteridine analogues) into an RNA first on the 
computer and than exp.
   I created the new residues for AMBER but there are several problems:
1. the force field parameters are all taken from analogies with other 
structures already existent in AMBER
2. I calculated the charges using Gaussian (STO-3G and 6-31G*) first for 
the base alone and than I tried with the whole residue. There are 
significant differences. I did not do a RESP fitting yet.
3. I did geometry optimization with Gaussian but the amino group of 2AP 
was not planar anymore.
4. I put all the residues in a simple AMBER minimizer but the energy 
landscape looks very funny in the sense that it fluctuates a lot before 
convergence.
5. I tried also some MD.

I have a question: Can somebody give a hint which would be the correct 
procedure for building these new residues and how can I obtain a 
reliabile residue structure that I can use for introducing in the RNA 
later on.

Thanks a lot,
vlad

-- 
Vlad Cojocaru 
Max Planck Institut for Biophysical Chemistry 
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