VMD-L Mailing List

From: Gary Turner (turnerscientific_at_sbcglobal.net)
Date: Tue Nov 06 2018 - 14:44:59 CST

Many thanks, John.  I had to change my user name from G&L to GL, which
required a registry edit, but it worked and New Cartoon works now.

Regards,

Gary Turner

On 11/4/2018 6:59 PM, John Stone wrote:
> 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.
>