VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Sep 13 2007 - 09:04:08 CDT

On Thu, 13 Sep 2007, Roland Schmucki wrote:

RS> Hello!

hello roland,

RS> To get to know the features of VMD, I am studying the "VMD Images and
RS> Movies Tutorial".
RS> http://www.ks.uiuc.edu/Training/Tutorials/vmd-ref/imgmv/tutorial-html/node3.html
RS> However, in the second unit, "Working With Trajectories", I couldn't
RS> load the dna.psf and trajectory.dcd files correctly. When loading
RS> (file->new molecule->filename:dna.psf etc), none of the molecules was
RS> displayed, although no error in the VMD console window was shown (see

please note, that a .psf file contains no coordinate information
(check out the 0 under Frames in the VMD Main window). the .dcd
on the other hand has no information about the structure,
atom/residue/segment names, mass, charge etc but only coordinates
(and cell depending on version). so it will only show disconnected
atoms as dots (if at all). you have to load the .dcd 'into'
the .psf file and then it should work fine.

cheers,
   axel.

RS> below). I've tried that on a linux and windows workstation, but it
RS> didn't work neither of them. So, there's something I did the wrong way.
RS>
RS> Thank you for any help and suggestions!
RS>
RS> Roland
RS> 

-- 
=======================================================================
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.