Re: [AMBER] Water bridge formed between protein and ligand

Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Mon, 4 Apr 2022 10:25:54 -0400

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.
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 04 2022 - 07:30:02 PDT