From: Axel Kohlmeyer (
Date: Wed Jan 16 2008 - 12:58:17 CST

On Wed, 16 Jan 2008, Sergey Mkrtchyan wrote:

SM> Hey Axel, thanks for the reply!
SM> Well, by saying not properly I mean it displays some particles (much more than
SM> I have lines in my file) spreaded in a weird way on a plane. I plot the same
SM> coordinates with gnuplot and see that it is fine.

yep. that confirms it.

SM> Do I understand you correct that just making an output file (I use C) with the
SM> appropriate "format" (columns, spaces, etc) and just renaming that to *.pdb
SM> won't work? Then how do you guys generate pdb files from an x,y,z ?

VMD writes .pdb files via the molfile plugin library.
the pdb standard is described on the pdb database webpages.

but in your case, i would just create XYZ/xmol style files
instead (unless you want to specify connectivity, too).
this format is much simpler:
1st line: number of atoms
2nd line: title, energy (is ignored by most codes)
3-nth line: atoms in the form: element x y z
here there are no fixed positions.


SM> Cheers,
SM> Sergey
SM> On January 16, 2008 01:26:08 pm Axel Kohlmeyer wrote:
SM> > please explain "not properly".
SM> > from the looks of it, my first guess is that your
SM> > "pdb" file is not according to the PDB standard.
SM> > please note, that .pdb is not "some columns" but
SM> > is formatted fortran with specific columns for
SM> > specific information and VMD honors that.
SM> >
SM> > cheers,
SM> >    axel.

Axel Kohlmeyer
   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.