From: Vlad Cojocaru (
Date: Sat Dec 13 2014 - 07:11:42 CST

Sorry .. This was my mistake .. the subopt program should be run with
0-based indices as well ...


On 12/13/2014 01:40 PM, Vlad Cojocaru wrote:
> Dear all,
> I encountered a problem with the network view plugin ....
> I performed a dynamic network analysis and at the last stage I run
> "subopt" to calculate the pathways between 2 nodes in the network. To
> run subopt I used the index number of the 2 nodes from the "carma.psf"
> file that was generated in the first stage from the original all-atom
> psf file ...
> Then I used the original all-atom PSF file to visualize the pathways
> using the NetworkView plugin. However, I noticed the when I calculate
> paths between nodes of lets say residue 100 and 200, the networkView
> plugin draws the paths between residues 101 and 201 (only one network
> node per residue) ...
> I thought that the output of subopt is according to the "carma.psf"
> file and this will be translated to the correct indices in the
> original all-atom PSF, of course taking into account that when
> visualizing, VMD will actually count from 0
> Did anybody notice this behavior ? Is this a bug in the plugin or am I
> missing something here ?
> Best wishes
> Vlad

Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]