From: Gumbart, JC (
Date: Tue Mar 01 2022 - 13:30:26 CST

Hi Syeda,

Unfortunately, the hbonds plugin wasn’t written with this level of specificity in mind. In fact, I took that part of the plugin from someone else’s contributed code. It might not be too difficult to modify to give more detailed information though; you can find it in the plugins/hbonds/ directory wherever your copy of VMD is installed.


On Feb 28, 2022, at 4:38 AM, SYEDA SABIHA SULTANA LUBNA . <<>> wrote:


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

The information contained in this electronic communication is intended solely for the individual(s) or entity to which it is addressed. It may contain proprietary, confidential and/or legally privileged information. Any review, retransmission, dissemination, printing, copying or other use of, or taking any action in reliance on the contents of this information by person(s) or entities other than the intended recipient is strictly prohibited and may be unlawful. If you have received this communication in error, please notify us by responding to this email or telephone and immediately and permanently delete all copies of this message and any attachments from your system(s). The contents of this message do not necessarily represent the views or policies of BITS Pilani.