AMBER Archive (2002)

Subject: new RNA residues

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Thu May 02 2002 - 14:07:32 CDT

<x-flowed>
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: Vlad.Cojocaru_at_mpi-bpc.mpg.de  

</x-flowed>