AMBER Archive (2002)

Subject: new residues

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Thu Apr 04 2002 - 07:03:37 CST

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Hello fellows AMBER users.
   I created four new residues for RNA. After I calculated the charges
in g94 I tried to put them in a simple AMBER minimizer (see below). What
I found out looking at the total energy profile after the minimization
is that the energy has a strange fluctuation. It has quite big jumps
during the minimization. I thought that my residues might be wrong in
some ways and I looked at a normal RG residue with the same minimizer.
Surprisingly in had the same behavior.
  Can you please take a look at my sander input file and tell me if it
is ok or not. If it is ok can you tell me why such behavior and if it is
not ok can you suggest me some adjustments that I could make?

This is the input file:

&cntrl
      imin=1, ntf=1, igb=3, dielec=4.0, ntb=0, cut=999.0,
      scnb=2.0, scee=1.2,
      maxcyc=50000, ncyc=50, ntmin=1, dx0=0.001, dxm=0.05,
      drms=0.05, ntpr=10, dele=0.000001,
   &end
 
Thanks for your help,
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  
Home Address: Gutenbergstrasse 26/8  
              37075 Goettingen, Germany 
Home tel. number: ++49-551-9963204
Mobile: ++49-179-6851586
alternative email: johhnny_ar_at_yahoo.com

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