The* hbond *command in cpptraj can help in finding bridging water. Check
that -
Ex:- hbond ligand_mask protein_mask solventdonor :WAT solventacceptor
:WAT.O bridgeout file.dat
Pancham
On Mon, Sep 25, 2017 at 6:17 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
> Hi,
>
> I want to check that my ligand in the system is forming a water bridge or
> not.
>
> By the term water bridge I mean an interaction between ligand - Water -
> protein is happening or not.
>
>
> Is there any way of analysis that can help me. if it forms then how long
> it is forming in my trajectory file.
>
>
> I have tried by observing the lowest energy structure but I am unable to
> find any such interactions.
>
>
> I have also tried clustering by using cpptraj, but here the problem is the
> structure of protein, ligand, and waters looks distorted.
>
>
>
> Any suggestion will be highly appreciated.
>
>
>
>
>
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Received on Mon Sep 25 2017 - 17:30:02 PDT
