From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Nov 04 2018 - 20:59:58 CST

Hi,
  The "&" character is not legal for many filesystem path implementations,
and the most likely issue here is that STRIDE and/or Tcl can't handle it.
I would suggest that you do your work in a path/directory somewhere
that doesn't contain that "G&L" directory, which is the cause of the
problem.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Nov 03, 2018 at 10:40:19AM -0700, Gary Turner wrote:
> I load VMD (Ver 1.9.3), and the molecule 1ubq.pdb (the file used in
> the tutorial) using Molecule File Browser.  Molecule loads in Tube
> representation.  Change to New Cartoon and I get:
>
> "Error reading PDB file C:\Users\G" (Correct path is
> C:/Users/G&L/Downloads/VMD/vmd-tutorial-files/1ubq.pdb.  Note that
> VMD used this path successfully 17 lines above in the attached
> VMD.exe output).
>
> I am attaching the VMD.exe output "VMD error on call to New Cartoon.txt"
>
> I have loaded the program on two desktops and a laptop, all Windows
> 10 (Ver 10.0.17134 Build 17134), all show the same problem.  I've
> tried several other molecules with the same result; an error and the
> representation remains Tube.  I've tried putting the .pdb files in
> different folders, including the root.  Same result. Any suggestions
> would be highly appreciated.
>

> Info) VMD for WIN32, 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
> 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) Free system memory: 4095MB (100%)
> Info) Creating CUDA device pool and initializing hardware...
> Info) Detected 1 available CUDA accelerator:
> Info) [0] GeForce GTX 645 3 SM_3.0 @ 0.82 GHz, 1.0GB RAM, KTO, AE1, ZCP
> Info) OpenGL renderer: GeForce GTX 645/PCIe/SSE2
> Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVFGS)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (16384x16384), 3-D (2048x2048x2048), Multitexture (4)
> Info) No joysticks found. Joystick interface disabled.
> Info) Dynamically loaded 75 plugins in directory:
> Info) C:/Program Files (x86)/University of Illinois/VMD/plugins/WIN32/molfile
> vmd > Info) Using plugin pdb for structure file C:/Users/G&L/Downloads/VMD/vmd-tutorial-files/1ubq.pdb
> Info) Using plugin pdb for coordinates from file C:/Users/G&L/Downloads/VMD/vmd-tutorial-files/1ubq.pdb
> Info) Determining bond structure from distance search ...
> Info) Analyzing structure ...
> Info) Atoms: 660
> Info) Bonds: 608
> Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> Info) Residues: 134
> Info) Waters: 58
> Info) Segments: 1
> Info) Fragments: 59 Protein: 1 Nucleic: 0
> Info) Finished with coordinate file C:/Users/G&L/Downloads/VMD/vmd-tutorial-files/1ubq.pdb.
> Info) In any publication of scientific results based in part or
> Info) completely on the use of the program STRIDE, please reference:
> Info) Frishman,D & Argos,P. (1995) Knowledge-based secondary structure
> Info) assignment. Proteins: structure, function and genetics, 23, 566-579.
> Error reading PDB file C:\Users\G
> The system cannot find the path specified.
> The system cannot find the path specified.
> ERROR) Unable to find Stride output file: C:\Users\G&L\AppData\Local\Temp\3
> ERROR) Stride::read_stride_record: unable to read output file from Stride
> ERROR) Call to Stride program failed.

-- 
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/