VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Feb 07 2008 - 22:16:18 CST

On Feb 7, 2008 10:58 PM, Tony Sheh <sheh_at_umich.edu> wrote:
> When a molecule is loaded, a bond is "computed" between each atom. Is
> there a way to turn this computation off, but still be able to specify
> connectivity?

tony,

you can change the bonding pattern interactively (see the mouse menu)
or with scripts via atom selections and setbonds subcommand. you can
write a program that creates a .psf or similar file with bonding information,
that would override the heuristics.

cheers,
   axel.

>
> Cheers,
> Tony
>
> 

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