From: mason H (
Date: Mon Sep 01 2014 - 13:27:25 CDT

I am performing Dynamical Network Analysis on my protein. I am using the
built-in 'networkSetup' VMD script. One residue is one 'node'.
I have a question on >RESTRICTIONS that get listed in the networkSetup
input file.

In most procedures I have seen so, they use the 'NotNeighboringResidue' and
'NotSameResidue' restriction.

Except for 'NotSameResidue', Is it ever ok to have NO restrictions when
looking at networks within a protien? Why can I not allow for edges
between consecutively numbered residues?

(FYI: In my case, my protein is 400 residues and, for the record, I am
looking at optimal and suboptimal paths between two different regions of a
protein about 25 Angstroms apart. I am wondering why I would prevent a
path from traversing along consecutively numbered residues)

Thank you,