VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Feb 13 2004 - 10:52:02 CST

Hi,
  I was just able to reproduce this problem with VMD 1.8.2 on
a different test Mac. As Justin says, it doesn't occur with the
newest builds of VMD, but I'm not sure why not. I get the same
md5sum he got, so that means there is genuinely something going amiss
in the gromos plugin, or in VMD 1.8.2 somewhere. I'll let you know
when I track this down further.

  John

On Fri, Feb 13, 2004 at 07:50:21AM -0800, Justin Gullingsrud wrote:
> 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
> >>
>
> --
> The universe is transformation: life is opinion. -- marcus aurelius 

-- 
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