VMD-L Mailing List

From: Jim Nettles (jnettle_at_emory.edu)
Date: Thu Feb 12 2004 - 23:25:20 CST

I'm also having the problem displaying the .gro file that Paul sent me.
Here is the output on my machine.

Last login: Thu Feb 12 13:53:35 on ttyp1
/Applications/VMD1.8.2/VMD\ 1.8.2.app/Contents/MacOS/startup.command;
exit
Welcome to Darwin!
[jnettle-5:~] nettles% /Applications/VMD1.8.2/VMD\
1.8.2.app/Contents/MacOS/startup.command; exit
Info) VMD for MACOSX, version 1.8.2 (December 4, 2003)
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, 1 CPU detected.
Info) OpenGL renderer: ATI Radeon 7000 OpenGL Engine
Info) Features: STENCIL RN MTX TCM
Info) Textures: 2-D (1024x1024), 3-D (128x128x128), Multitexture (3)
vmd > Info) Using plugin gro for structure file
/Users/nettles/Data/Concoord/Tubulin/Barret/tub_taxol/
average_structure.gro
Info) Using plugin gro for coordinates from file
/Users/nettles/Data/Concoord/Tubulin/Barret/tub_taxol/
average_structure.gro
Info) Finished with coordinate file
/Users/nettles/Data/Concoord/Tubulin/Barret/tub_taxol/
average_structure.gro.
Info) Analyzing structure ...
Info) Atoms: 864
Info) Residues: 864
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 864 Protein: 0 Nucleic: 0

Thanks,

Jim Nettles

P.S.

This is a 667Mhz Titanium G4 Powerbook I'm running 10.2.8

16MB ATI(AGP) Card Model ATY,RageM6
On Thursday, February 12, 2004, at 06:22 PM, John Stone wrote:

>
> Paul,
> I had no trouble loadin the .gro file you emailed me on my VMD test
> Mac here, so it makes me wonder if there's something unusual about
> your machine there. If you do in fact get the right count of atoms,
> then its possible that its a graphics related problem of some kind.
> Can you send me the VMD startup messages that your machine prints
> when you run it? On my test Mac the structure you sent looks exactly
> the
> same as it does on Solaris, Linux, etc.
>
> Thanks,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Feb 10, 2004 at 01:56:50PM -0000, barrett wrote:
>> Hi
>>
>> I'm finding different behaviour between the Linux and Apple versions
>> of
>> VMD that is causing me a problem.
>>
>> I have a gromacs .gro file that contains only the C-alphas of a
>> protein.
>> In the linux version I can import the file and it shows up fine,
>> either
>> in lines, or tube or vdw representation or whatever.
>>
>> In the apple version although it loads without error, and shows that
>> the
>> molecule contains the right number of atoms in the main menu I cant
>> get
>> it to be displayed in the display.
>>
>> It works fine for pdbs.
>>
>> Is this familiar? Any suggestions anyone?
>>
>>
>> Many thanks
>>
>> Paul
>>
>>
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078