AMBER Archive (2004)

Subject: AMBER: Extracting torsional angles for specific conformation

From: Darian, Eva (EJD1_at_cdc.gov)
Date: Wed Nov 03 2004 - 12:12:33 CST

Dear amber users,
 

I have a peptide that goes from extended to bended conformation during
MD run. I collect unformatted trajectory and monitor the conformation
change by measuring end to end distance (N 1 to C 5) with carnal. I
want to extract torsional angles from the frames corresponding to the
bent conformation only, i.e. for the structures that have end to end
distance 5 angstrom or less. Is it possible to do with carnal, or any
other means?

 
Thanks
Eva.

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