new RNA residues

From: Vlad Cojocaru <>
Date: Thu 02 May 2002 21:07:32 +0200

I have created new residues ready for introducing them in RNA. The
approach was the following:
  -I created the residue starting with one already existing (ex: 2amino
purine starting from adenine)
  -I derived the missing parameters using antechamber from Amber7.
  -The charges were derived using two stage RESP fit.
  -The residues were them introduced in a simple AMber minimizer in
vacuum using an igb=3(distance dependent) and a dielectric constant
equal to 4.
I have 2 questions:
  -The total energy obtained from the minimization is positive. What is
the significance of such values for the total energy?
  -Does anyone tried this kind of an approach and if yes can anybody
give me some ideeas how to prove the consistency of the models that I
have created? How could I prove that they are correct?
  I have already received some answers to this matter and I want to
thank for all.
Best regards,

Vlad Cojocaru 
Max Planck Institut for Biophysical Chemistry 
Deparment: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1389 
Received on Thu May 02 2002 - 12:07:32 PDT
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