Author Topic: How to calculate the number of H-Bonds  (Read 122 times)

Sahari

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How to calculate the number of H-Bonds
« on: April 28, 2019, 08:16:40 PM »
Dear all,

I want to calculate the number of hydrogen bonds in a system and to do so, I need to apply the bond and angle criteria (assuming 30 degrees and 3.5 Angstrom) for h-bond formation between the atoms. I know that I should write some python scripts, but actually, I couldn't come up with the idea of how to check the angle and the length of the non-covalent bond between Donor-H-Acceptor atoms involved in a hydrogen bond. I really appreciate any help. Btw, I use the latest version of Ovito. Thanks in advance.

Best,
Sahar

Constanze Kalcher

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Re: How to calculate the number of H-Bonds
« Reply #1 on: April 29, 2019, 12:29:36 PM »
Dear Sahar,

I don't have a good understanding of your system yet, but it sounds like you could use the Create bonds modifier with pairwise cutoffs to first find all neighbors of each hydrogen atom within a cutoff of 3.5 Angström.
Then you could have a look at this topic, where it is discussed how to calculate bond angles. In principle you could write a custom python script modifier that calculates bond angles for all Donor-H-Acceptor pairs
http://forum.ovito.org/index.php?topic=265.msg2069#msg2069
and then create a selection for only those pairs that fulfill your bond angle criterion.

-Constanze
« Last Edit: April 29, 2019, 01:02:40 PM by Constanze Kalcher »