From: Raul Araya (arayasecchi_at_gmail.com)
Date: Mon Apr 14 2008 - 12:01:41 CDT

Dear VMD users:

This question might be out of the scope of this mailing list, but I really
need help.
I have a DCD trajectory file composed of a tetramer of a protein, lipids,
waters and ions
and I want to generate separate trayectories of each monomer alone. I cant
do it in VMD
because the DCD file is very large (8+ GB) to be loaded in the memory of my
machine, I want to use
catDCD but I dont really understand how can one select the atoms in catDCD.
The example states :
"-i <indexfile>indexfile should contain the (zero-based) indices of the
atoms in the dcd
files whose coordinates are to appear in the output file. The indicesshould
be ASCII text, separated by whitespace."

but I dont quite understand what are the "(zero-based) indices of the atoms
in the dcd"
Can any one help me please...

-- Raúl Araya Secchi B.Sc Molecular Biotechnology. Molecular Biotechnology
Engineer. Centre for Bioinformatics CBUC, Faculty of Biological Sciences, P.
Universidad Catolica de Chile Portugal # 49 – ZIP 6513492 Santiago – Chile
Phone: + 56 2 6862269; http://www.cbuc.cl