Date: Tue Mar 01 2022 - 14:58:06 CST

Hi Syeda,

When we were doing detailed hydrogen bond analyses, nothing beat (at the time) charmm itself;
If you are in a position to use charmm, I’d be happy to share files to help get you started.


> On Feb 28, 2022, at 1:38 AM, SYEDA SABIHA SULTANA LUBNA . <> wrote:
> 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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