VMD-L Mailing List

From: Mike McCallum (mmccallum_at_PACIFIC.EDU)
Date: Wed Jul 26 2017 - 09:50:28 CDT

Hello, I want to make a correction: this issue does NOT exist in vmd 1.9.4a7.
Cheers
Mike

On Jul 25, 2017, at 9:40 PM, Mike McCallum <mmccallum_at_PACIFIC.EDU<mailto:mmccallum_at_pacific.edu>> wrote:

Hi there,
I’m not quite sure when this happened, but I am unable to get ‘mol pdbload’ to work. I tried this with 1.9.2, 1.9.3 and 1.9.4a versions on OS X, new and old versions of the OS. I’m running a class right now and I’m asking the students to do this, so help is much appreciated. Here is the startup info + error.
—
Info) VMD for MACOSXX86, version 1.9.3 (November 30, 2016)
Info) 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, 8 CPUs detected.
Info) OpenGL renderer: NVIDIA GeForce GT 650M OpenGL Engine
Info) Features: STENCIL MDE CVA 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 1.9.3.app/Contents/vmd/plugins/MACOSXX86/molfile
vmd > The PDB is supported by RCSB, the NSF, US PHS, NIH, NCRP, NIGMS, NLM,
and US DoE, who are not liable for the data. PDB files shall not be
sold. See ftp://ftp.rcsb.org/advisory.docT3ZCORN2OPOYRoy7n7U&e=> for full details.
Info) Using plugin webpdb for structure file 1anv
ERROR) BaseMolecule: init_atoms called with invalid number of atoms: 0
ERROR) molecule_structure: Unable to read structure for molecule 0
ERROR) molecule_structure: severe error indicated by plugin aborting loading of molecule 0
Info) Using plugin webpdb for structure file 1sse
ERROR) BaseMolecule: init_atoms called with invalid number of atoms: 0
ERROR) molecule_structure: Unable to read structure for molecule 1
ERROR) molecule_structure: severe error indicated by plugin aborting loading of molecule 1
--

Cheers
Mike

--
C. Michael McCallum
Professor
Department of Chemistry, UOP
mmccallum .at. pacific .dot. edu (209) 946-2636 v / (209) 946-2607 fax






--
C. Michael McCallum
Professor
Department of Chemistry, UOP
mmccallum .at. pacific .dot. edu (209) 946-2636 v / (209) 946-2607 fax