VMD-L Mailing List

From: Bennion, Brian (bennion1_at_llnl.gov)
Date: Thu Jun 18 2015 - 11:03:48 CDT

Hello Axel,

I left out the fact that these pdb files are very general and lack any atom type info. I all have to work with is atom name, element, and what VMD guesses for bonds.

Brian

-----Original Message-----
From: Axel Kohlmeyer [mailto:akohlmey_at_gmail.com]
Sent: Wednesday, June 17, 2015 5:34 PM
To: Bennion, Brian
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: differentiate between nitroso and oxime atomselections

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.