VMD-L Mailing List

From: Josh Vermaas (vermaasj_at_msu.edu)
Date: Thu Aug 18 2022 - 08:29:35 CDT

Basically, it is 180-a from your figure. The angle is defined as the
angle between two vectors. In Measure.C from the VMD source, this is the
relevant code:

vec_sub(donortoH,hydrogen,coor2);
vec_sub(Htoacceptor,coor1,hydrogen);
if (angle(donortoH, Htoacceptor)  < maxangle ) {

The first command computes the vector from the hydrogen to the donor,
and stores it in donortoH. The second command computes the vector from
the acceptor to the hydrogen. The angle between those vectors ends up
being 180-a from your diagram. Since a=150.something, 29 is too strict,
since 180 -150.something > 29, but 30 works.

-Josh

On 8/18/22 6:41 AM, David Carrasco de Busturia wrote:
> This question refers to the `Angle Cutoff` variable for hydrogen bonds
> detection in vmd.
>
> Consider the water dimer posted here:
> https://urldefense.com/v3/__https://github.com/DavidCdeB/H-bonds__;!!DZ3fjg!6eelqv3K_FVBrC7uk35RBqGl_-WWd26i8n0CDiOriaYrWj3OuaZNXYPBatW2POtSRzkZ19yk_L3SiSSEIfM$
> <https://urldefense.com/v3/__https://github.com/DavidCdeB/H-bonds__;!!DZ3fjg!_zzd0T13G69_pKop_G6jmXTL9LemaGAIpEaeoRyf-Q_jq74VTn7zdzB7NA8umDEY9371WXK9tnqgOyH_KD0ZLJ4s5Zmu$>
>
> I've marked the `a`, `b` and `c` angles for the hydrogen bond.
> (where the numeric values shown are those that appear in the terminal
> window when measuring them with vmd).
>
> The hydrogen bond is not detected for `Angle Cutoff = 29`|| but it is
> detected for `Angle Cutoff = 30` (see figures in the post)
>
> I'm wondering which is this `Angle Cutoff`|| that VMD is referring to
> since 30 does not seem to match any of the angles marked in the image.
> 

-- 
Josh Vermaas
vermaasj_at_msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
vermaaslab.github.io