VMD-L Mailing List

From: mason H (tailermason_at_gmail.com)
Date: Tue Sep 30 2014 - 20:22:31 CDT

Hello,
   I am working with an enzyme that is a dimer. I performed 'Dynamical
Network Anaysis' on the enzyme. For each subunit, I generated a "contact
map" (--- that is, I have two subunits, and I have two contact.dat files).

   I am now doing pathway analysis (using 'subopt').

   When I look at the pathway between two nodes on one subunit, it produces
a certain set of 'pathways.'
    When I look at the pathway between the same two nodes in the other
subunit, the pathways are similar, with some slight differences.

    I noticed that 'subopt' uses the 'contact.dat' file.

Can I average the data from my two 'contact.dat' files to produce one
"Average_contact.dat" file? -- Can I then perform subopt on this average
contact map to create average pathways?

 I know this is technically feasible (I have done it) -- but is it
"allowed?"

 As long as I also separately report the pathways of each subunit (perhaps
in "supplemental info") Can I display the "average" pathway data in a
report?

Thank you