VMD-L Mailing List

From: Richard Swenson (swenson_at_hec.utah.edu)
Date: Mon Apr 14 2008 - 13:28:19 CDT

Raúl,

 

You should be able to use catDCD to create the trajectories you want.
Zero-based means that the list of atoms in the system starts at 0 instead of
1. I use a tcl script in VMD to write the index file and a reduced psf file
with a script like this:

 

*******************

package require psfgen

topology ../toppar/top.inp

 

readpsf mypsf.psf

coordpdb mypdb.pdb

mol load psf mypsf.psf pdb mypdb.pdb

 

set all [atomselect top “all”]

set sel1 [atomselect top “the atoms I want”] --for examples replace the
text with “segname M1”, “water”, etc.

set sel2 [atomselect top “not [$sel1 text]”]

 

set indices [$sel1 get index]

 

set file [open findexfile.ind w]

foreach I $indices {

            puts $file $i

}

 

flush $file

close $file

foreach segid [$sel2 get segid] [$sel2 get resid] atomname [$sel2 get name]
{

            delatom $segid $resid $atomname

}

 

writepsf $newpsf.psf

exit

 

*******************

 

Good luck,

 

Richard

 

 

  _____

From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
Raul Araya
Sent: Monday, April 14, 2008 11:02 AM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: catDCD

 

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 <http://www.cbuc.cl/>