VMD-L Mailing List

From: Александр Кошкаров (steuermannako_at_gmail.com)
Date: Thu Dec 20 2018 - 02:53:47 CST

Dear all,

I faced a problem analyzing a protein in dimeric form with Dynamical
Network Analysis implemented in
VMD. When I follow the tutorial with aaRS:tRNA complex, everything works
well. Moreover, it's Ok
when I use a monomer of my protein. The problem is rising when I use the
homo-dimer and is that no
dynamical network appears in the second subunit, while in the first one it
exists. Visualization of the
trajectory after NetworkSetup disturbs both covalent bonds in the second
subunit although all the
atoms are in correct position (in correspondence with those of the first
subunit) and its dynamical
network (a few nodes and no connections are shown).
I got a trajectory with GROMACS. All the residues in two subunits had
different numbers. The topology
topol.top file was constructed using gmx2pdb with a -merge flag to avoid
the appearing of #include links
in the topology file. When using catdcd, the .xtc trajectory was converted
to .dcd. Topology file was
converted using the top2psf.pl script by Mark Baaden. Converted topology
and trajectory were used for
Dynamical Network Analysis.

Which step could be incorrect?
How to build the dynamical network between two subunits in the dimer?

Any help and suggestions are very appreciated.

best regards,
Koshkarov Alexandr.