VMD-L Mailing List

From: Payman Pirzadeh (ppirzade_at_ucalgary.ca)
Date: Thu May 16 2013 - 14:46:23 CDT

Hello,
I perform my simulations with GROMACS 4.5.4. I want to perform a
dynamical network analysis on my trajectory. I converted the
processed .top file into .psf using 'top2psf.pl' script, and I used VMD
to save my .xtc trajectory in .dcd format.
I changed the network.config, which in the same folder as my .psf
and .dcd files, as follow:
>Psf
/system.psf

>Dcds
/system.dcd

>SystemSelection
chain A

>NodeSelection
(name CA)

>Clusters
  
>Restrictions
notSameResidue
notNeighboringCAlpha

On the tkConsole, I ran into errors about .psf file, which could not be
open. I used 'autopsf' module and generated the psf file using the
processed .top file; I should mention that during generating the .psf
file, everything went OK except for the time I clicked "I'm feeling
lucky" that a complicated error message popped up. But the .pfs file was
already written, and things looked OK in it. I changed the
systemselection to P1, and still it cannot read the .psf file.
I am left wonder what I should do?
All hints and tips are appreciated.
Best,

Payman