VMD-L Mailing List

From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Fri Nov 11 2022 - 14:24:10 CST

Hi Nick,

I think modifying the existing code for your purposes will be the easiest course of action. You can find it in the plugins directory wherever your VMD is installed. To test without re-starting vmd, you can type “package forget hbonds” followed by “package require hbonds”.

Best,
JC

On Nov 10, 2022, at 5:57 PM, Nick Bayhi <bayhi_at_uchicago.edu<mailto:bayhi_at_uchicago.edu>> wrote:

Hello,

The hbonds plugin<https://www.ks.uiuc.edu/Research/vmd/plugins/hbonds/> is very useful for my analysis, but its output format could be more convenient:

By default, the plugin provides a file with # of Hbonds between my selections at each frame, OR an overall "Details" file describing % occupancy of a given pair across a trajectory.

What I want, is the detailed information (Hbond donor, Hbond acceptor identity) at each frame for all of a given trajectory.

Right now, my solution is to run the Hbonds script for each frame of my trajectory, creating a unique Details file at each frame (with 100%+ occupancy). I then modify the Details files with a Linux script (and add a column for molecule name and frame #), and import them all into one giant data frame in R for subsequent analysis. But this import of so many files takes a long time!

Is the code for this plugin available somewhere, so I can modify it for my purposes?
Or, would you recommend creating a brand new script instead?

My desired output would look something like this (bold is new) with data from the whole simulation:

Molecule / Frame / Donor / Acceptor / Occupancy
...
Protein1 / 997 / Segs0-GLN1234-Main / Segs0-ASN1324-Main / 100.0%
Protein1 / 998 / Segs0-GLN1234-Main / Segs0-ASN1324-Main / 100.0%
Protein1 / 998 / Segs0-ASN1235-Main / Segs0-PHE1975-Main / 100.0%
Protein1 / 999 / Segs0-ASN1235-Main / Segs0-PHE1975-Main / 100.0%
...
Or perhaps, Molecule could be the inputs of "Sel1" and "Sel2"

Any advice would be welcome!

PS -- I'll probably want to do this with the salt bridges<https://www.ks.uiuc.edu/Research/vmd/plugins/saltbr/> plugin as well...

--
Nick Bayhi
(971) 219-7408
Wei-Jen Tang Lab<https://urldefense.com/v3/__https://voices.uchicago.edu/wtang-lab/__;!!DZ3fjg!6SP9ke-bdtkY6F80cFuuqF1JWkUao8qcyUJFY__5XQsWmsWD6WqjBSgHngBg-OkB7A02oDx1_vDmm5w9tzc$>
Biophysical Sciences
University of Chicago