VMD-L Mailing List

From: Sergey Mkrtchyan (sergeyvmd_at_gmail.com)
Date: Wed Jan 16 2008 - 13:53:09 CST

On January 16, 2008 01:58:17 pm Axel Kohlmeyer wrote:
>
> 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.
>
> cheers,
> axel.

Thanks a lot for the help, that format worked out for me (with some minor
unfulfilled desires, like display of the chain as a "trace").

I'll try to figure out that with pdb too...

Thanks again!

Sergey

p.s. Sorry Axel, I didn't mean to sent this message to private 

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