VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jan 17 2012 - 13:19:21 CST

On Tue, Jan 17, 2012 at 1:26 PM, Ganesh Kamath <gkamath9173_at_gmail.com> wrote:
> I have set the angle.

that wasn't my point. i was just pointing out that the distance
is a necessary but not sufficient condition for a hydrogen bond.
you only had manually checked for the distance.

> 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.

huh? you wrote you wanted hydrogen bonds.

> 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.

the hbond plugin is just a wrapper for the "measure hbond"
command. all conditions that apply to that command, apply
to the GUI a well.

> Could you please suggest or help.

have you made sure that the selection listed
as the hbond "donor" actually donates hydrogen bonds?

have you checked that your hydrogens are bonded
to the donor selection atoms?

have you made sure that VMD can detect your hydrogens
as hydrogens?

do the hbonds show up with the HBond representation?

axel.

> 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.
> 

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