From: Ganesh Kamath (gkamath9173_at_gmail.com)
Date: Tue Jan 17 2012 - 12:26:01 CST

I have set the angle. My question is whether, the hbond analysis can compute
hydrogen bonds between individual atoms of the chain as specified.

I want to compute the distance between Nitrogen on the bmim ring and
the oxygen present on the anion.
Towards that I use this:
Selection 1 : resname BMI and type NR1
Selection 2: resname F2N and type OBT

However, I get no output at all. the hbond.dat is filled with zeroes.

Could you please suggest or help.

thanks!

---------- Forwarded message ----------
From: Axel Kohlmeyer <akohlmey_at_gmail.com>
Date: Mon, Jan 16, 2012 at 6:13 PM
Subject: Re: vmd-l: Question regarding HBond analysis
To: Ganesh Kamath <gkamath9173_at_gmail.com>
Cc: vmd-l_at_ks.uiuc.edu

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.