VMD-L Mailing List

From: Alvea Tasneem (alveatasneem21_at_gmail.com)
Date: Thu Mar 24 2022 - 12:47:24 CDT

Hello,

I am having an issue in running the wat_hbond.tcl script. The script
[attached below] calculates all hydrogen bonds between a donor and an
acceptor selection, returns the water oxygen atoms, and selects the full
residue afterward. Currently, the selections are made for resid of waters
as well as added a column that shows frame number.

However, one issue arising from this script is that it returns all the
water molecules that make hbond with either one or more residues, depending
upon the selection of acceptor atom is more than one residue. For example,
in my case I have the acceptor selection- *name N and resid 143 144 145*,
and donor selection- *water*. The output it is giving me is this *W6746
W1856 W7068*. Here, only the water ID 7068 makes hbond with N atom of all
three residues. Whereas water IDs 6746 and 1856 make hbond with N atom of
145 and 143, respectively.
I only need those water molecules that make hbond with all the residues
mentioned in the selection and not with one residue, i.e. water Id 7068.
Therefore, are there any changes that I must make in the script to get this
kind of result?
I will look forward to your reply.
Thank you.