Thank you for your suggestion. But can we check any water molecule forming bridge between protein and ligand by using cpptraj ? like protein-water-ligand. example LYS-water-SO3, here LYS is protein part whereas SO3 is ligand part, so can we analyse water as a bridge between protein and ligand by using cpptraj?
Please suggest if there is any way to calculate water bridge between two solute. Thank you in Advance.
----- Original Message -----
From: "Daniel Roe" <daniel.r.roe.gmail.com>
To: "amber" <amber.ambermd.org>
Sent: Monday, April 4, 2022 7:55:54 PM
Subject: Re: [AMBER] Water bridge formed between protein and ligand
On Mon, Apr 4, 2022 at 9:39 AM Shakuntala Dhurua <518cy6026.nitrkl.ac.in> wrote:
> which I am not looking for,
We could probably help better if you describe what you are looking for
specifically.
> Is there any other way of analyzing protein-water-ligand bridges? and also what does it mean which was generated in out file All.bridge.avg.dat. Please help me to understand.
Please read the 'hbond' command entry in the Amber or Cpptraj manuals
(e.g.
https://jenkins.jasonswails.com/job/amber-github/job/cpptraj/job/master/lastSuccessfulBuild/artifact/doc/CpptrajManual.pdf).
You might try the 'bridgebyatom' keyword which will report bridging
results by atom instead of by residue. If you use the GitHub version
of cpptraj (
https://github.com/Amber-MD/cpptraj) you can use the
recently added bridging time series keywords (see
https://github.com/Amber-MD/cpptraj/pull/948) to get a time series for
each detected bridge.
Hope this helps,
-Dan
>
> Any help will be highly appreciated. Thank you in advance.
>
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Received on Mon Apr 04 2022 - 10:30:02 PDT
