AMBER Archive (2003)

Subject: Hbond analysis with Carnal

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Fri Mar 21 2003 - 08:50:36 CST

Hi there,
  I have also a question about the Carnal output with respect to the
Hbond analysis.
  The ".lis" file contains all the distances and angles for Hbonds as
long as they are occupied.
Lets say for instance that I have a Hbond that is occupied 50% during
the trajectory and I would like to monitor the distance and angle not
only when it is occupied but also when it is not. Is there a way to do
that within Carnal? or could ptraj do that? Or I have to separately
calculate the distance and angle?
Best regards,
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