AMBER Archive (2004)

Subject: AMBER: nucleic acid bases nonplanar during LES sim

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Mon Feb 02 2004 - 15:17:09 CST

Dear ambers,
   Visualizing first LES trajectories for an RNA fragment (for one copy
out of 5) I noticed that the nucleic bases are not planar. Does that
mean that the impropers were not applied? Is that a reason to worry
about the simulation?
 Thank you very much
vlad 

-- 
Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
home tel: ++49-551-9963204  

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