Subject: new RNA residues

From: Vlad Cojocaru <[email-masked]>
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

-- 
Vlad Cojocaru 
Max Planck Institut for Biophysical Chemistry 
Deparment: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1389 
e-mail: [email-masked]