VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Feb 20 2020 - 13:24:56 CST

Did you do "make distrib" step to copy the plugins from the compile
area into the form used for the VMD installation image? You have to have
a PLUGINDIR environment variable set, and normally you'd symlink from
that area into vmd/plugins, so that when you do "make_distrib" in the
VMD build area, it will pick up the install-ready plugin tree as needed.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Feb 20, 2020 at 02:13:47PM -0500, Joe Konecny wrote:
> Can anyone confirm what the plugin directory is supposed to look
> like? After an apparently successful compile and install here is what I
> see...
>
> (I've linked it with pastebin because it's a large tree listing)
>
> In ~/vmd-1.9.4a38/plugins
>
>
> https://pastebin.com/HrmQMTYs
>
>
>
>
>
>
> On 2/19/20 2:00 PM, John Stone wrote:
> >Hi,
> > I've got to run to a meeting, but you're a reasonable fraction of
> >the way there. It appears that something went wrong in terms of your
> >compilation/installation of the VMD plugins, but otherwise the startup
> >messages are fairly reasonable. I don't think a Pi can handle GLSL, so
> >that's no surprise.
> >
> >Best,
> > John
> >
> >On Wed, Feb 19, 2020 at 10:39:31AM -0500, Joe Konecny wrote:
> >>I have absolutely zero knowledge on what vmd does but a friend asked
> >>me to get it running on raspberry pi. So I did but I noticed a few
> >>messages on startup that makes me wonder if it will work correctly
> >>for him. Mainly with GLSL rendering and packages that could not be
> >>loaded. Can anyone comment on these messages and how they will
> >>affect the ability of vmd to do what it's supposed to do?
> >>
> >>
> >>pi_at_raspberrypi:~/vmd-1.9.4a38/LINUXAARCH64ARM $ ./vmd_LINUXAARCH64ARM
> >>Info) VMD for LINUXAARCH64ARM, version 1.9.4a38 (February 19, 2020)
> >>Info) http://www.ks.uiuc.edu/Research/vmd/
> >>Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> >>Info) Please include this reference in published work using VMD:
> >>Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> >>Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> >>Info) -------------------------------------------------------------
> >>Info) Multithreading available, 4 CPUs detected.
> >>Info) Free system memory: 3695MB (94%)
> >>Warning) Detected X11 'Composite' extension: if incorrect display occurs
> >>Warning) try disabling this X server option. Most OpenGL drivers
> >>Warning) disable stereoscopic display when 'Composite' is enabled.
> >>Warning) Simple graphics mode: OpenGL 1.0, no extensions
> >>Info) OpenGL renderer: V3D 4.2
> >>Info) Features:
> >>Info) GLSL rendering mode is NOT available.
> >>The irspecgui package could not be loaded:
> >>
> >>The multiseq package could not be loaded:
> >>
> >>The networkview package could not be loaded:
> >>
> >>The pmepot_gui package could not be loaded:
> >>
> >>The autoionizegui package could not be loaded:
> >>
> >>The solvate package could not be loaded:
> >>
> >>The autopsf package could not be loaded:
> >>
> >>The cggui package could not be loaded:
> >>
> >>The dowser_gui package could not be loaded:
> >>
> >>The chirality_gui package could not be loaded:
> >>
> >>The cispeptide_gui package could not be loaded:
> >>
> >>The forcefieldtoolkit package could not be loaded:
> >>
> >>The mdff_gui package could not be loaded:
> >>
> >>The membrane package could not be loaded:
> >>
> >>The mergestructs package could not be loaded:
> >>
> >>The molefacture package could not be loaded:
> >>
> >>The mutator package could not be loaded:
> >>
> >>The alascan package could not be loaded:
> >>
> >>The autoimd package could not be loaded:
> >>
> >>The qwikmd package could not be loaded:
> >>
> >>vmd > Info) Using plugin pdb for structure file /home/pi/m.pdb
> >>Info) Using plugin pdb for coordinates from file /home/pi/m.pdb
> >>Info) Determining bond structure from distance search ...
> >>Info) Analyzing structure ...
> >>Info) Atoms: 17
> >>Info) Bonds: 16
> >>Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> >>Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> >>Info) Residues: 2
> >>Info) Waters: 0
> >>Info) Segments: 1
> >>Info) Fragments: 1 Protein: 1 Nucleic: 0
> >>Info) Finished with coordinate file /home/pi/m.pdb.
> >>Info) VMD for LINUXAARCH64ARM, version 1.9.4a38 (February 19, 2020)
> >>Info) Exiting normally.
> > 

-- 
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/