VMD-L Mailing List

From: Ciara McCormack (cmccormack11_at_qub.ac.uk)
Date: Thu Jul 04 2013 - 04:17:14 CDT

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