VMD-L Mailing List

From: Jernej Zidar (jernej.zidar_at_gmail.com)
Date: Tue Sep 27 2011 - 22:34:53 CDT

Alternatively you can instruct CHARMM to save the coordinate file with
the COR extension instead of the CRD. Technicaly it's just a matter of
replacing "crd" with "cor" in the input file.

Renaming the files from CRD to COR would accomplish the same. You can
do the renaming using a short bash script like:
ls *.crd | while read var; do mv $var ${var%%.crd}.cor ; done

I've been using the aforementioned methods for the last three/four
years without any problem.

Regards,
Jernej

On Wed, Sep 28, 2011 at 10:08, Vadim Patsalo <patsalov_at_gmail.com> wrote:
> Hello VMD mailing list,
>
> I am a CHARMM user. I find myself having to constantly type:
>
>    vmd -cor X.crd -cor Y.crd -cor Z.crd
>
> when trying to load multiple CHARMM CRDs into the same molecule. I would like to overwrite the default VMD behavior of associating the .crd file extension with the Amber7 CRD plugin, and instead associate it with the COR plugin.
>
> I've attempted to create a symbolic link from crdplugin.so to corplugin.so in
>    /Applications/VMD\ 1.9.app/Contents/vmd/plugins/MACOSXX86/molfile/      (Mac OS X)
>
> However, this does nothing. It doesn't appear that VMD uses the dynamic libraries inside ../molfile/, and is even able to recognize .crd files as Amber7 CRD when the crdplugin.so file is moved.
>
> Is there a way to correct this behavior at startup inside .vmdrc? I am open to other hackety suggestions. One possibility is to write a wrapper script which takes as input "vmd A.crd B.crd C.crd" and runs the system command "vmd -cor A.crd -cor B.crd -cor C.crd", I suppose. Renaming the files to .cor is not a real option for me.
>
> Thanks in advance!
> Vadim
> 

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