VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Jan 16 2012 - 18:13:55 CST

On Mon, Jan 16, 2012 at 6:05 PM, Ganesh Kamath <gkamath9173_at_gmail.com> wrote:
> Hi All,
>
>  I am having certain issues regarding atom selection using HBOND plugin. I am
> trying to determine the hbond  between two atoms NR1 and OBT belonging to the
> cation BMI and anion TF2N as a function of the entire trajectory.
>
> Selection 1 : resname BMI and type NR1
> Selection 2: resname F2N and type OBT
>
> Donor acceptor distance =3.2
> Angle cutoff = 20
>
> I click on All hbonds.
>
> I get a data vector empty. But if I look at the frames there are atoms
> NR1 within 3 A of OBT.

but distance is only one of the two criteria that make a hydrogen bond.

axel.

>
> Can some one please advise.
>
> Thanks for your time.
>
> Regards,
> ganesh 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.