AMBER Archive (2002)

Subject: carnal averaging

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Mon Sep 02 2002 - 06:43:33 CDT

Dear Amber users,
    Does anybody know what is wrong with the output from a simple CARNAL
averaging. The pdb file of the average structure can not be visualized
with any software and I also can not use it afterwards for calculating
the rmsd of each frame to the average structure. The script is below:
FILES_IN
   PARM p1 ../rna_ion_wat.top;
   STREAM s1 ../00.crd.gz ../01.crd.gz ../02.crd.gz ../03.crd.gz
../04.crd.gz;
  
FILES_OUT
   COORD crd AVG.pdb PDB;
DECLARE

OUTPUT
   COORD crd s1 AVERAGE;

END 

-- 
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