VMD-L Mailing List

From: Alvea Tasneem (alveatasneem21_at_gmail.com)
Date: Wed Feb 02 2022 - 11:48:23 CST

Hello,
I need to check which water molecules (MD simulations) with their specific
water IDs are coming at the catalytic pocket of my protein within hydrogen
bond distance in each frame (in my case, I have 2500 frames to check),
i.e., in each frame which water ID is making hydrogen bond with the
residues.
I have tried using Hydrogen Bond plugin tool of VMD, however, it only gives
me the general name Water-O and no particular water ID like, TIP39116
If I start checking every frame manually then it becomes a tedious job. So,
I am eagerly looking for a TCL script by which I can identify the specific
water ID of all frames.
To be more specific regarding my problem, I am hereby attaching the
*hbond.dat* and *hbond-details.dat *output files from Hydrogen Bond plugin
tool of VMD.
I am eagerly waiting for your kind help and suggestions.
Thank you for your consideration.