VMD-L Mailing List

From: Kirby Vandivort (kvandivo_at_ks.uiuc.edu)
Date: Tue Jul 09 2013 - 11:29:29 CDT

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