VMD-L Mailing List

From: Sophie Mader (sophie.mader_at_tum.de)
Date: Tue Jun 26 2018 - 04:27:04 CDT

Dear all,

I would like to analyze the network of an MD simulation.
In order to reduce the file size, I included only backbone heavy atoms in my
trajectory (N, CA, C, O), as well as 2 ATP molecules and 4 magnesium ions.
My psf file has the following format:

PSF

       1 !NTITLE
  REMARKS VMD-generated NAMD/X-Plor PSF structure file

5508 !NATOM
       1 AP 1 MET N NH3 -0.300000 14.0070 0
       2 AP 1 MET CA CT1 0.210000 12.0110 0
       3 AP 1 MET C C 0.510000 12.0110 0
       4 AP 1 MET O O -0.510000 15.9990 0
                                           :
                                           :
                                           :

I would like to follow the "Dynamical Network Analysis" tutorial.
My "network.config" file looks like this:

>Psf
./backbone_ATP.psf
>Dcds
./backbone_ATP.dcd
>SystemSelection
all
>NodeSelection
name CA or (resname ATP and name N9 PG) or name MG
>Clusters
N9 ATP name C4' O4' C1' C5 N7 C8 N9 N1 C2 N3 C4 C6 N6 C2' O2' C3' O3' C5' O5'
PG ATP name PG O1G O2G O3G PB O1B O2B O3B PA O1A O2A O3A
>Restrictions
notSameResidue
notNeighboringCAlpha
notNeighboringPhosphate

When I open VMD and type "networkSetup network.config" into the TkConsole, I
get the following error message:
"Error: not possible to build nodeSelString: () and ()"

Could somebody give me a hint what I have to change in my setup?

Many thanks in advance
Sophie Mader