VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Feb 26 2007 - 17:26:38 CST

On Mon, 26 Feb 2007, Nichols A. Romero wrote:

nichols,

if you export to anything that has atom types you first have to
load a corresponding file with that information (e.g. an .xyz, .psf,
.pdb), do an 'animate delete all' and then load your .dcd file and
write it out in a different format. the corresponding plugins in VMD
should not crash in this case, but i've seen similar crashes before
when loading files without atom information (e.g. when clicking on
them in the OpenGL window).

you may also want to look into the 'catdcd' package...

axel.

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

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.