VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Mon Sep 22 2014 - 19:35:07 CDT

Worked like a charm. :D

And your explanation made sense with the header error.

Thanks for your help.

On Tue, Sep 23, 2014 at 12:08 PM, Josh Vermaas <vermaas2_at_illinois.edu>
wrote:

> Hi Ashar,
>
> If the output filetype isn't dcd, you are required to specify the output
> filetype, as the default is dcd. What you did with catdcd is make a
> dcd-formatted file with a .xtc extension. You can test this by
> force-loading the "xtc" file you made into VMD as a dcd, and it will work.
> So your command line should be:
>
> catdcd.exe -o ala.trr -otype trr -dcd alanin.dcd
>
> catdcd also can't write xtc files (at least according to its usage
> information, that's why the command above outputs to trr), as the
> molfileplugin for xtc doesn't have a writer, only a reader.
>
> -Josh Vermaas
>
>
> On 09/22/2014 06:07 PM, Ashar Malik wrote:
>
> Hi,
>
> I have data in DCD trajectories. I need to use something in the gromacs
> package, one way of which is to convert dcd to xtc/trr.
>
> I use -
>
> catdcd.exe -o ala.xtc -dcd alanin.dcd
>
> which gives this:
>
> CatDCD 5.2
> dcdplugin) detected standard 32-bit DCD file of opposite endianness
> dcdplugin) X-PLOR format DCD file (also NAMD 2.0 and earlier)
> Opening file 'ala.trr' for writing.
> dcdplugin) detected standard 32-bit DCD file of opposite endianness
> dcdplugin) X-PLOR format DCD file (also NAMD 2.0 and earlier)
> Opened file 'alanin.dcd' for reading.
> Read 100 frames from file alanin.dcd, wrote 100.
> Total frames: 100
> Frames written: 100
> CatDCD exited normally.
>
> alanin.dcd is a 66 atom 100 frame trajectory in the VMD install, which I
> am using to test the system.
>
> ala.xtc is then visualized using VMD which is where the problem emerges
> (if it is a problem).
>
> In the VMD install there is a alanin.pdb holding 66 atoms. That is
> loaded into VMD and ontop of that I try to load the xtc file that I just
> made.
>
> Error: Unable to load molecule (in the vmd gui)
>
> at the backend in the command line the shell is showing:
>
> gromacsplugin) Cannot read header from '(file path).xtc', no error
> ERROR) Couldn't read file (same path as above)
>
> Question: Did CatDCD mess up - or is it the way I am loading the
> structure.
> Question: A missing header means (usually) trajectory wasn't made
> correctly. Right ?
> Question: If I pass both (pdb/xtc) of these files to Gromacs, and it by
> chance works, is the system trustable ?
>
> My system specs are 32-Bit windows running CatDCD 32-bit 5.2.
>
> Any help would be appreciated.
>
> Best,
> /A
>
>
>
> --
> Best,
> /A
>
>
> 

-- 
Best,
/A