VMD-L Mailing List

From: Joe Konecny (joe_at_freakyacres.com)
Date: Thu Feb 20 2020 - 13:32:45 CST

Yeah I ran make distrib. That tree listing was PLUGINDIR which is
/home/pi/vmd-1.9.4a38/plugins and not the plugin src directory. This is
what I assume make distrib created. Why is the symlink needed? Doesn't
make distrib just cp everything?

PLUGINDIR=/home/pi/vmd-1.9.4a38/plugins

On 2/20/20 2:24 PM, John Stone wrote:
> 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.
>>>
>