VMD-L Mailing List

From: ivana adamovic (iadamovic_at_gmail.com)
Date: Thu Feb 01 2007 - 13:17:21 CST

Dear John,

It seems that my laptop has 3-D option:

Info) OpenGL renderer: ATI Radeon X1600 OpenGL Engine
Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (4096x4096), 3-D (256x256x256), Multitexture (8)
Plugin directory '/Users/ivana/testplugins/MACOSXX86/molfile'
does not exist!
vmd >
==============

So I have tried CHARMM example again (with 1.8.5 VMD) and there is
just white surface: ERROR) Cannot read file of type pbeq:

vmd > play 1kdx.vmd
Info) Using plugin pdb for structure file 1kdx_charmm.pdb
Info) Using plugin pdb for coordinates from file 1kdx_charmm.pdb
Info) Determining bond structure from distance search ...
Info) Finished with coordinate file 1kdx_charmm.pdb.
Info) Analyzing structure ...
Info) Atoms: 1815
Info) Bonds: 1838
Info) Residues: 109
Info) Waters: 0
Info) Segments: 2
Info) Fragments: 2 Protein: 2 Nucleic: 0
0
ERROR) Cannot read file of type pbeq
Unable to load file '1kdx.pbeq' using file type 'pbeq'.
Info) No volume data loaded at index 0
Reading 1815 atoms..done
Probe radius = 1.400
Constructing solvent-accessible surface ..
Max edge length = 1.200
unusual malloc(0)

Could you please tell me where to get new test versions of VMD 1.8.6
(or plugin update 1 for 1.8.5) ? I have checked on BioCore web page
but can't find Mac (Intel core) version of VMD 1.8.6?

Also could you please tell me what : Plugin directory
'/Users/ivana/testplugins/MACOSXX86/molfile' does not exist! from the
vmd start up tells me ?

I guess I either need VMD 1.8.6 or the update you have mentioned for
VMD 1.8.5 in order to be able to see CHARMM elec. potential ...

Thanks a lot,

Ivana