VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 03 2018 - 11:14:40 CDT
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- In reply to: Sophie Mader: "AW: Error: not possible to build nodeSelString: () and ()"
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Hi,
I didn't write this tool, it was written by others, but looking at
the code, it seems that the error message you have encountered occurs
when either the "system" selection or the "node" selection string are empty.
You listed both selections below, but perhaps there's a typo of some kind
in your input file. I would recommend that you double check that everything
is spelled correctly since the code that reads the config file is very
specific and won't accept any deviation from its expected formatting.
Best,
John Stone
vmd_at_ks.uiuc.edu
On Thu, Jun 28, 2018 at 12:37:02PM +0000, Sophie Mader wrote:
> Dear all,
>
> just if anybody comes across the same problem: It is essential to have
> blank lines in the "network.config" file inbetween the different parameter
> definitions:
>
> ----------------------------
>
> >Psf
> backbone_ATP.psf
>
> >Dcds
> backbone_ATP.dcd
>
> >SystemSelection
> all
> >NodeSelection
> name CA or (resname ATP and name N9 PG) or name MG
> ----------------------------
>
> Best regards
>
> Sophie Mader
>
> --------------------------------------------------------------------------
>
> Von: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> im Auftrag von
> Sophie Mader <sophie.mader_at_tum.de>
> Gesendet: Dienstag, 26. Juni 2018 11:27:04
> An: vmd-l_at_ks.uiuc.edu
> Betreff: vmd-l: Error: not possible to build nodeSelString: () and ()
>
>
> 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
-- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/
- Next message: John Stone: "Re: Inorganic builder in no display mode - Reg"
- Previous message: Axel Kohlmeyer: "Re: How to define charge group and pass it to topo writegmxtop"
- In reply to: Sophie Mader: "AW: Error: not possible to build nodeSelString: () and ()"
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