VMD-L Mailing List

From: Dani (dani.rivas.r_at_gmail.com)
Date: Wed Mar 16 2016 - 16:50:47 CDT

Thanks to both of you. Somehow your answers ended up in my spam and I wasn't able to read it before. I solved this myself, just loading both dcd files one after the other and saving them in a new dcd file, together. But, it's good to know I can try this for another time.

Thanks!
Daniela.

> El 04-03-2016, a las 21:49, Josh Vermaas <vermaas2_at_illinois.edu> escribió:
>
> 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> 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.
>