VMD-L Mailing List

From: Nick Fisher (nefisher_at_msu.edu)
Date: Fri Oct 31 2014 - 10:51:09 CDT

The OpenGL display window of VMD 1.9.1 (non-CUDA) is freezing immediately after loading a set of PDB coordinates in a fresh install of OS X 10.10

I’m using a late-2012 Mac Mini (8 Gb RAM, 2.5 GHz i5, Intel HD 4000 graphics). The spinning VMD logo freezes, and the molecule is not displayed. Here’s the console log (note that the program does not crash, it is just unusable):

Info) VMD for MACOSXX86, version 1.9.1 (February 4, 2012)
Info) http://www.ks.uiuc.edu/Research/vmd/ <http://www.ks.uiuc.edu/Research/vmd/>
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu <mailto: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) OpenGL renderer: Intel HD Graphics 4000 OpenGL Engine
Info) Features: STENCIL MDE MTX NPOT PP PS GLSL(OVF)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (16384x16384), 3-D (2048x2048x2048), Multitexture (8)
Info) Dynamically loaded 2 plugins in directory:
Info) /Applications/VMD 1.9.1.app/Contents/vmd/plugins/MACOSXX86/molfile
vmd > Info) Using plugin pdb for structure file /Applications/Bowman bc1 /1SQP.pdb
Info) Using plugin pdb for coordinates from file /Applications/Bowman bc1 /1SQP.pdb
Info) Determining bond structure from distance search ...
Info) Analyzing structure ...
Info) Atoms: 17274
Info) Bonds: 17481
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 2329
Info) Waters: 215
Warning) Unusual bond between residues: 83 (protein) and 382 (none)
Warning) Unusual bond between residues: 37 (protein) and 243 (none)
Info) Segments: 1
Info) Fragments: 236 Protein: 11 Nucleic: 0
Info) Finished with coordinate file /Applications/Bowman bc1 /1SQP.pdb.