VMD-L Mailing List

From: Nichols A. Romero (naromero_at_gmail.com)
Date: Mon Feb 26 2007 - 17:03:54 CST

John,

Thanks for your whick reply. The DCD file was created with QS which is part
of CP2K (cp2k.berlios.de).

Axel Kohlmeyer helped with the programming of the plugin I believe.

The steps are
1. New Molecule
2. Load the DCD file
3. Click on the Molecule and do "Save Coordinates"
4. Save to XYZ and POSCAR leads to a core dump.

If I save out to another DCD file, it does *NOT* crash though.

I just also tested PDB and that seems to crash as well, like XYZ and POSCAR.

I could probably even create a small DCD file that you could play around
with. The one I am working
with is too big to e-mail (even with compression).

On 2/26/07, John Stone <johns_at_ks.uiuc.edu> wrote:
>
>
> Hi,
> Can you tell me the exact sequence of steps you're performing, and
> what program generated the original DCD file? Do you get the same
> behavior
> if you save back out to another DCD file, or is this problem only
> associated
> with formats such as XYZ etc?
>
> John
>
> On Mon, Feb 26, 2007 at 05:28:41PM -0500, Nichols A. Romero wrote:
> > Oops... I forgot to mention that those sequence of operations cause VMD
> to
> > crash.
> >
> > On 2/26/07, Nichols A. Romero <naromero_at_gmail.com> wrote:
> > >
> > >Hi,
> > >
> > >I am reporting a bug in VMD 1.8.5. I am running RHEL on an Intel 32-bit
> > >system. I also have nVIDIA video card
> > >but I don't believe any of these details are relevant since I can
> > >reproduce this problem on SGI Altix (IA64)
> > >system as well which is quite different from my desktop machine.
> > >
> > >I am simply loading a Trajectory in DCD format and then trying to
> export
> > >the coordinates to ANY format, e.g.
> > >xyz, POSCAR, etc. I have run with the debug option and this is what I
> get.
> > >
> > >
> > >(gdb) where
> > >#0 0x0051b600 in strncpy () from /lib/tls/libc.so.6
> > >#1 0x08142465 in MolFilePlugin::write_structure ()
> > >#2 0x081020c7 in CoorPluginData::CoorPluginData ()
> > >#3 0x0817219a in VMDApp::molecule_savetrajectory ()
> > >#4 0x081b7186 in SaveTrajectoryFltkMenu::do_save ()
> > >#5 0x083bde7c in Fl_Button::handle ()
> > >#6 0x083ba310 in fl_throw_focus ()
> > >#7 0x083ba402 in Fl::handle ()
> > >#8 0x083cd057 in fl_handle ()
> > >#9 0x083cc66e in Fl::remove_fd ()
> > >#10 0x083cc890 in fl_wait ()
> > >#11 0x083b9bb6 in Fl::wait ()
> > >#12 0x0816e1fd in VMDApp::VMDupdate ()
> > >#13 0x08184857 in main ()
> > >
> > >
> > >
> > >
> > >
> > >--
> > >Nichols A. Romero, Ph.D.
> > >1613 Denise Dr. Apt. D
> > >Forest Hill, MD 21050
> > >443-567-8328 (C)
> > >410-306-0709 (O)
> > >
> >
> >
> >
> > --
> > Nichols A. Romero, Ph.D.
> > 1613 Denise Dr. Apt. D
> > Forest Hill, MD 21050
> > 443-567-8328 (C)
> > 410-306-0709 (O)
>
> --
> 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
> 

-- 
Nichols A. Romero, Ph.D.
1613 Denise Dr. Apt. D
Forest Hill, MD 21050
443-567-8328 (C)
410-306-0709 (O)