VMD-L Mailing List

From: Sergey Mkrtchyan (sergeyvmd_at_gmail.com)
Date: Wed Jan 16 2008 - 12:39:31 CST

Hey Axel, thanks for the reply!

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

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

Cheers,
Sergey

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

-- 
Sergey Mkrtchyan,
PhD Student @
Department of Physics & Astronomy,
Faculty of Science, University of Waterloo