Hi,
Probably your best bet would be to use the 'hbond' command with
'series' and 'solventacceptor :WAT.O' keywords to generate time series
data for waters interacting with the Zn (make sure the distance cutoff
is set to around 3.5, set angle cutoff to -1 to disable), followed by
'lifetime' analysis to measure the lifetime of 'bound' states. See the
manual for full command details. A very very basic example of this is
given in the following tutorial:
https://amberhub.chpc.utah.edu/hydrogen-bond-analysis-within-a-protein/
Maybe others have a better idea. Hope this helps,
-Dan
On Wed, May 3, 2023 at 10:19 AM Dulal Mondal via AMBER
<amber.ambermd.org> wrote:
>
> Dear Users,
>
> I have a trajectory and a prmtop file. I am trying to calculate the
> residence time of water molecules.
> How long do water molecules remain in a sphere of radius 3.5 angstrom
> centered from the Zn atom?
>
> Thanking you
>
>
>
> --
> *With regards,*
> *Dulal Mondal,*
> *Research Scholar,*
> *Department of Chemistry,*
> *IIT Kharagpur, Kharagpur 721302.*
> _______________________________________________
> 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 Fri May 05 2023 - 12:30:02 PDT
