VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Apr 14 2008 - 12:08:34 CDT

On Mon, 14 Apr 2008, Raul Araya wrote:

RA> Dear VMD users:

dear raul,

RA> This question might be out of the scope of this mailing list, but I really
RA> need help.

since catDCD is utilizes VMD's molfile plugins, it sortof fits in.

RA> I have a DCD trajectory file composed of a tetramer of a protein,
RA> lipids, waters and ions and I want to generate separate trayectories
RA> of each monomer alone. I cant do it in VMD because the DCD file is
RA> very large (8+ GB) to be loaded in the memory of my machine, I want
RA> to use

first off, you don't have to load the whole file. you could just
load a part and convert that, then skip over that part and convert
the next part and so on.

RA> catDCD but I dont really understand how can one select the atoms in catDCD.
RA> The example states :
RA> "-i <indexfile>indexfile should contain the (zero-based) indices of the
RA> atoms in the dcd
RA> files whose coordinates are to appear in the output file. The indicesshould
RA> be ASCII text, separated by whitespace."
RA>

RA> but I dont quite understand what are the "(zero-based) indices of
RA> the atoms in the dcd"

the index numbers are exactly what VMD (internally) uses as index.

so if you load a .psf and a single frame of your system, you can then
create a selection for each subsystem that you want to look at and
then do a "get index" on that to retrieve the information you need.

e.g.

set prot [atomselect top "protein"]
$prot get index

cheers,
   axel.

RA> Can any one help me please...
RA>
RA> -- Raśl Araya Secchi B.Sc Molecular Biotechnology. Molecular Biotechnology
RA> Engineer. Centre for Bioinformatics CBUC, Faculty of Biological Sciences, P.
RA> Universidad Catolica de Chile Portugal # 49 ? ZIP 6513492 Santiago ? Chile
RA> Phone: + 56 2 6862269; http://www.cbuc.cl
RA> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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If you make something idiot-proof, the universe creates a better idiot.