VMD-L Mailing List
From: Kirby Vandivort (kvandivo_at_ks.uiuc.edu)
Date: Tue Jul 09 2013 - 11:29:29 CDT
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Ciara,
My suspicion is that your system selection and node selection are causing the
PSF file to actually not have any atoms.
What happens when you load the files manually into VMD and do an atomselect..
mol load psf system.psf
mol addfile system.dcd last 0
set sel [atomselect top "((chain A) and (not hydrogen)) and ((name CA))"]
$sel num
If you are getting zero, that indicates that there actually are no atoms.
Kirby
On 07/04/2013 04:17 AM, Ciara McCormack wrote:
>
> Hello,
>
> I want to perform dynamical network analysis on a protein using the networkView
> plugin. I saved my trajectory file, a trr. in dcd format using VMD and converted
> my .pdb file to a .psf file using psfgen which generated a psf file through VMD.
>
> I changed the network.config which is in the same folder as my .psf and .dcd
> files, as follow:
>
> />Psf /
> /system.psf
>
> />Dcds /
> /system.dcd
>
>
> />SystemSelection /
> (chain A) and (not hydrogen)
>
>
> />NodeSelection /
> (name CA)
>
>
> />Clusters /
>
> />Restrictions /
> notSameResidue
> notNeighboringCAlpha
>
>
> When in the tkConsole I ran the command networkSetup network.config the
> following error message appeared:
>
> ?[37m?[1mcarma
> v.1.2?[4;37m____________________________________________________________________?[0m
>
> ?[31m?[1mPSF file without an NATOM card ? Abort.?[0m
> child process exited abnormally
>
>
> Any advice or tips would be appreciated.
>
> Regards,
> Ciara
>
-- Kirby Vandivort Theoretical and Senior Research Programmer Computational Biophysics Email: kvandivo_at_ks.uiuc.edu 3061 Beckman Institute http://www.ks.uiuc.edu/~kvandivo/ University of Illinois Phone: (217) 244-5711 405 N. Mathews Ave Fax : (217) 244-6078 Urbana, IL 61801, USA
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