VMD-L Mailing List
From: Richard Swenson (swenson_at_hec.utah.edu)
Date: Mon Apr 14 2008 - 13:28:19 CDT
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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/>
- Next message: Axel Kohlmeyer: "Re: catDCD"
- Previous message: Peter Freddolino: "Re: topology files L/D form"
- In reply to: Raul Araya: "catDCD"
- Next in thread: Axel Kohlmeyer: "Re: catDCD"
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