AMBER Archive (2002)

Subject: carnal output trajectory

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Thu Oct 24 2002 - 15:07:35 CDT

Dear AMBER and VMD users,
   I am trying to visualize a AMBER trajectory made with carnal using vmd
If I take each trajectory and unzip as it was row created by AMBER
everything is fine but if I load into vmd the trajectory outputed by
carnal it loads something really strange. Could somebody tell why this
behaviour?
The input files for CARNAL are:

FILES_IN
   PARM p1 ../../rna_ion_wat.top;
   STREAM s1 ../../rna_ion_wat_mdeq_final.mdcrd.gz;
FILES_OUT
   COORD crd movie.mdcrd;
DECLARE
   GROUP g1 (RES 1-17);
   IMAGE img g1%cmass;
OUTPUT
   COORD crd s1 MOD 10;
END

and:

FILES_IN
   PARM p1 ../../rna_ion_wat.top;
   STREAM s1 ../../rna_ion_wat_mdprd00.mdcrd.gz
         ../../rna_ion_wat_mdprd01.mdcrd.gz
         ../../rna_ion_wat_mdprd02.mdcrd.gz
         ../../rna_ion_wat_mdprd03.mdcrd.gz
         ../../rna_ion_wat_mdprd04.mdcrd.gz
         ../../rna_ion_wat_mdprd05.mdcrd.gz
         ../../rna_ion_wat_mdprd06.mdcrd.gz;
FILES_OUT
   COORD crd movie.mdcrd APPEND;
DECLARE
   GROUP g1 (RES 1-17);
   IMAGE img g1%cmass;
OUTPUT
   COORD crd s1 MOD 50;
END

Is there another way to select certain frames from a suite of
trajectories???
Thanks a lot for any replies!
Best wishes,
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