From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Fri Mar 04 2016 - 18:49:23 CST

Hi Daniela,

It looks like you are running it from within the VMD tkconsole. The
generated execution line that exectools is calling looks wrong:
/home/daniela/Downloads/vmd-1.9.2/plugins/LINUXAMD64/bin/catdcd5.1/catdcd -stridedinamica_cristal2.dcd
-i dinamica_cristal.dcd -o dinamica_cri...

What I would do is run it like this:

/home/daniela/Downloads/vmd-1.9.2/plugins/LINUXAMD64/bin/catdcd5.1/catdcd -o
outputfilename.dcd inputfile1.dcd inputfile2.dcd

That is the syntax that works for me. In principle, you don't need an
index file.

-Josh Vermaas

On 3/4/16 5:21 PM, Chitrak Gupta wrote:
> Hi Daniela,
>
> I am not positive, but I have a feeling you need to specify a index
> file or structure file. I usually do the latter, i.e. a PSF file (I
> already have PSF files as I run my simulations using NAMD). I don't
> remember from the top of my head what an index file is, but in any
> case, I think catdcd needs something more than just the DCD files to
> understand what your system is (how many atoms, etc).
>
> Hope this helps,
> Chitrak.
>
>
>
> On Wed, Mar 2, 2016 at 1:11 PM, Daniela Rivas <dani.rivas.r_at_gmail.com
> <mailto:dani.rivas.r_at_gmail.com>> wrote:
>
> Hello,
>
> I'm trying to concatenate two dcd files using this command line:
>
> catdcd -o dinamica_cristal_completa.dcd dinamica_cristal.dcd
> dinamica_cristal2.dcd
>
> and I'm getting the following error:
>
> -code 1 -level 0 -errorcode {CHILDSTATUS 1910 1} -errorinfo
> {CatDCD 5.1
> Reading indices from file 'dinamica_cristal.dcd'
> Error: no indices found in file.
> while executing
> "::exec
> /home/daniela/Downloads/vmd-1.9.2/plugins/LINUXAMD64/bin/catdcd5.1/catdcd
> -stride dinamica_cristal2.dcd -i dinamica_cristal.dcd -o
> dinamica_cri..."
> ("eval" body line 1)
> invoked from within
> "eval ::exec [list $exec_path] [lrange $args 1 end]"
> (procedure "::ExecTool::exec" line 14)
> invoked from within
> "::ExecTool::exec catdcd -stride $stride -i $indexFile -o $outFile
> $dcdFileNames"
> ("eval" body line 1)
> invoked from within
> "eval ::ExecTool::exec {catdcd -stride $stride -i $indexFile -o
> $outFile $dcdFileNames} "} -errorline 13
>
> Any ideas what I'm doing wrong? Am I using the right command line
> to concatenate?
>
> Cheers,
> Daniela.
>
>