Hi,
On Mon, Apr 4, 2022 at 1:24 PM Shakuntala Dhurua <518cy6026.nitrkl.ac.in> wrote:
>
> 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?
Yes, the SO3 should be picked up if you aren't specifying any
particular mask. Otherwise you can explicitly select it like:
hbond :SO3,<mask selecting protein>
You may also want to add the 'nointramol' keyword if you're not
interested in intramolecular hydrogen bonds. Hope this helps,
-Dan
>
> 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 Wed Apr 06 2022 - 07:00:02 PDT
