AMBER Archive (2002)

Subject: defining groups on dif. sets in carnal

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Tue Nov 19 2002 - 04:59:06 CST

Dear Amber users. I want to output a trajectory with carnal after
fitting. I also want to output only a group of atoms from my structure
so I am doing the following:

FILES_OUT
   COORD crd movie_rna.mdcrd;
DECLARE
   GROUP g1 s1 (RES 1-17);
   IMAGE img g1%cmass;
   RMS fit FIT g1;
   GROUP g2 fit (RES 1-17);
OUTPUT
   COORD crd fit GROUP g2;
END
EOF

Now, if I don't use the definition of group g2 and I use "COORD crd fit GROUP g1" in the output section the error mesage is telling me that the group g1 is not defined on the same set. Pretty normal since g1 is defined on s1 and I want to output on fit. But if I try to define g2 as in the script above the program is telling me :
"GROUP: unexpected tocken, last tocken fit"
The question is: Is it possible in carnal to define groups on different sets like in the script abouve or should I do it in 2 steps (taking more time and memory usage)
Thanks a lot for any replies,
Best wishes,
vlad 

-- 
Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1389 
e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
home tel: ++49-551-9963204