VMD-L Mailing List

From: Justin Gullingsrud (jgulling_at_mccammon.ucsd.edu)
Date: Fri Feb 13 2004 - 09:50:21 CST

Works for me with current source code; same video card. Just to be
sure we're looking at the same file, here's the output of "md5sum
problem.gro":

6fcf641fefe7bc290cf81bf1e8293744 problem.gro

Justin

On Feb 12, 2004, at 9:25 PM, Jim Nettles wrote:

> 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
>> 

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