VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jun 17 2015 - 19:34:09 CDT

On Wed, Jun 17, 2015 at 7:55 PM, Bennion, Brian <bennion1_at_llnl.gov> wrote:
> Hello,
>
>
>
> I may be over thinking my problem, but my atomselection fu is not cutting
> it.
>
>
>
> If a molecule has an oxime group O-N=C-R and a nitroso group O-N(=O)-R how
> would I select just the oxygen in the oxime portion of the molecule?
>
> Currrently, “oxygen and resname LIG and (not withinbonds 1 of carbon) and
> (withinbonds 1 of nitrogen)” selects all three oxygen atoms.

why use the generic "oxygen" to select the oxygen? why not use "name"
or "type" or a combination of it?
those should be more specific (but also dependent on an input
following conventions and force field typing).

axel.

>
>
>
> I don’t think a further distance selection would be wise, but maybe that is
> the route to take?
>
>
>
> Any suggestions?
>
>
>
> Brian
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.