From: Bennion, Brian (
Date: Tue Apr 09 2013 - 12:44:59 CDT

catdcd is faster than the using the code below, once you create the index file that removes the water.


-----Original Message-----
From: [] On Behalf Of Josh Vermaas
Sent: Tuesday, April 09, 2013 7:25 AM
Subject: Re: vmd-l: how to convert dcd to pdbs in command line

Another option is to run VMD in text mode. Make a simple script
(script.tcl) like this:

mol new psffile.psf
set nowater [atomselect top "not water"] for { set i 0 } { $i < 70000 } { incr i } {
    animate read dcd dcdfile.dcd beg $i end $i waitfor all
    $sel writepdb $i.pdb
    animate delete

This will go through each frame one by one and write it to its own pdb, while never keeping more than 1 frame in memory. You can then run it from the command line with something like:

vmd -dispdev text -e script.tcl (see for more on using the command line to start vmd, including the extra step required on windows)


On 04/09/2013 01:12 AM, wrote:
> Hey,
> Consider using ambertools ptraj for instance, which could do the pdb export.
> Best regards.
> Peter
> -----Message d'origine-----
> De : [] De la
> part de Yarrow Madrona Envoyé : mardi 9 avril 2013 01:43 À : VMD
> mailing list Objet : Re: vmd-l: how to convert dcd to pdbs in command
> line
> Hello,
> I am trying to convert a dcd to a series of pdb's without opening the
> VMD GUI. The reason is that I don't have enough ram to store the DCD
> (70,000
> frames) into memory. VMD always crashes unless I use a truncated DCD. I would like to use all frames since the frames will be analyzed by another software (Caver3.0). Is there a way to tell vmd to write out all PDBs in the command line (preferably without water although I can remove those later)?
> Thank you
> --
> Yarrow Madrona
> Graduate Student
> Molecular Biology and Biochemistry Dept.
> University of California, Irvine
> Natural Sciences I, Rm 2403
> Irvine, CA 92697