AMBER Archive (2002)

Subject: parameterization of a new class of compounds (nucleic acid base analogues)

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Mon Sep 09 2002 - 04:40:05 CDT


Dear Amber users,
   I have parameterized 5 base analogues for incorporation into RNA. I
am wondering if there is way to verufy how optimal the parameterization
is. For that I need the advice of somebody who previously parameterized
base analogues like 2 amino purine for instance. I would klike to know
how did you test the new parameters?
  I would also like to know the procedure for depositing the parameters
into the Amber data base.
   Thanks a lot in advance for any answers.
  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