VMD-L Mailing List

From: SYEDA SABIHA SULTANA LUBNA . (p20190061_at_hyderabad.bits-pilani.ac.in)
Date: Mon Feb 28 2022 - 03:38:01 CST

Hi,

I need a list of protein-RNA interaction via water molecules. For this i am
using Hydrogen bonds plugin in VMD. I have two issues:

1) When I am using the "all hbonds" option though its giving me the list,
its not giving the details of atoms involved in that interaction (as we get
in "unique bond" options).

2) Also, when I am trying to get the list of water molecule involved in
hbonds with protein, the file don't have the details of water molecule ID.

The two issues highlighted in red:
"Found 327 hbonds.
donor acceptor occupancy
SegAP1-ARG21-*Side * SegW-*water*-O 73.68%
SegBP1-LYS70-Side SegW-water-O 69.84%
SegAP1-ARG59-Side SegW-water-O 85.52%
SegAP1-LYS20-Side SegW-water-O 69.88%
SegBP1-ARG67-Side SegW-water-O 84.36%"

Can someone please help me solve this issue.

Thank you.
Syeda Lubna 

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