the amino group of 2amino purine has strange behaviour

From: Vlad Cojocaru <>
Date: Thu 12 Sep 2002 20:42:10 +0200

Dear Amber users,
   I replaced one residue from an RNA with 2-amino purine. Then I ran a
minimization with the molecule and what is happened is that the amino
group of 2AP is having a strange behaviour. The hydrogens are rotating
and the C2 N2 and H21 and H22 atoms are not planar anymore .
  So I thought well, might be that an improper torsion is missing. I
looked at the 99ff and I found the defined improper X-X-N2-H that I
guess is the improper that keeps the any amino group planar. I also set
in my frcmod file for base analogues the explicit torsion involving the
amino group (same as X-X-N2-H).
 I ran the minimization again and purely I observed the same movement.
So i got lost and could not explain why???? Now, the hydrogens of the
amino group tend to participate in some hydrogen bonding .
So, shortly I was wondering if anyone could explain this.
  I tried to attach a jpeg picture to this but it seems that I can not
send it. If somebody is interested to see a picture I can send it
Thanks a lot in advance,
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 Sep 12 2002 - 11:42:10 PDT
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