AMBER Archive (2002)

Subject: carnal output trajectory

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Wed Oct 30 2002 - 07:25:36 CST

Dear Amber users,
  I found out that OUTPUT COORD option in carnal has an option BOX which
is not written in the manual.
  With this option I managed to output trajectories in a proper way for
visualizing them with VMD.
  Now the question is that I want to see the trajectory after fitting
all the structures to the first frame.
  The BOX option seems not to work anymore when I give to carnal the
following:
DECLARE
   GROUP g1 (RES 1-17);
   IMAGE img g1%cmass;
   RMS fit1 FIT g1;
OUTPUT
   COORD crd fit1 BOX;
The program gives an error message that tells me that the BOX option
does not work with fit. If I do not use the BOX option the trajectories
are again impossible to visualize with VMD.
 Does anyone have any suggestions about this??
Thanks a lot!
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