VMD-L Mailing List

From: Nick Bayhi (bayhi_at_uchicago.edu)
Date: Thu Nov 10 2022 - 16:57:02 CST

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