VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue Apr 26 2016 - 20:45:09 CDT

Hi Anthony,

With such a loose cutoff, maybe. Is there a hydrogen on both the "donor"
and "acceptor", or perhaps 2 on the donor? My understanding is that
hbonds are drawn between the donor and acceptor if the heavy atoms are
within a certain distance (in your case 3.8 Angstroms), and the A-D-H
angle (acceptor-donor-hydrogen) is less than your cutoff (in this case
70 degrees). I would not be surprised if you could get two different
hydrogens to satisfy those constraints, and show up as two different lines.

-Josh Vermaas

On 04/26/2016 05:57 PM, Anthony Ma wrote:
> Hello,
>
> I'm emailing about a question regarding using the HBonds drawing
> method as a way to extract hydrogen bonds information for a
> trajectory. I have been able to use tcl commands to get the donor,
> acceptor pairs but there seems to be duplicates for the same frame.
> With the setting of 3.8 distance and 70 Angle cutoff there are two
> lines being drawn between (index 75594 or index 29778) query. I'm not
> sure how it's possible for two hydrogen bonds to form between just a
> single pair of atoms, but any help regarding this issue would be
> highly appreciated. Thanks!
>
> On Tue, Apr 26, 2016 at 12:55 PM, Anthony Ma <akma327_at_stanford.edu
> <mailto:akma327_at_stanford.edu>> wrote:
>
> Hello,
>
> I'm emailing about a question regarding using the HBonds drawing
> method as a way to extract hydrogen bonds information for a
> trajectory. I have been able to use tcl commands to get the donor,
> acceptor pairs but there seems to be duplicates for the same
> frame. With the setting of 3.8 distance and 70 Angle cutoff there
> are two lines being drawn between (index 75594 or index 29778)
> query. I'm not sure how it's possible for two hydrogen bonds to
> form between just a single pair of atoms, but any help regarding
> this issue would be highly appreciated. Thanks!
>
> anthony
>
>