AMBER: ptraj analyze modes question

From: Vlad Cojocaru <>
Date: Thu, 07 Oct 2004 15:17:02 +0200

Dear Amber users,
   I am trying to analyze the modes from PCA analysis by calculating the
rms fluctuation. I am using the following script:

trajin ../../comp_loop_P.mdcrd
analyze modes displ out displacement.dat file evecs.pev beg 1 end 1
analyze modes fluct out fluctuation.dat file evecs.pev beg 1 end 1
The problem is that my results are always printed on STOUT although I
gave an output file. Could somebody explain to me why?
The file evecs.pev is obtained with analyze matrix command.
Thank you very much

Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
home tel: ++49-551-9963204  
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Thu Oct 07 2004 - 14:53:00 PDT
Custom Search