Dear Damiano,
I can recommend you AQUA-DUCT, a small molecules tracking software, which
does exactly what you described.
It can provide you not only the number of O2 molecules that visited the
active site, but also the information about the exact pathway the molecule
entered the active site.
On the AQUA-DUCT website you can check the User Guide, and there's also a
recorded webinar from last year :)
http://www.aquaduct.pl/
Hope that helped!
Best regards,
Karolina
pon., 12 kwi 2021 o 18:51 Damiano Spadoni <Damiano.Spadoni.nottingham.ac.uk>
napisał(a):
> Dear AMBER users,
>
> I've run an MD simulation of an enzyme containing the cuboidal [4Fe-4S]
> cluster in the active site and the SAM molecule that coordinates to metal
> cluster.
> The same simulation contains O2 molecules within the water solvent. I am
> interested in looking at the number of O2 molecules that enter the active
> site and approach the metal cluster over the simulation and track the route
> of the identified O2 molecule(s).I looked at the possibilities to retrieve
> so by using cpptraj by I failed with the hbond command (because there is no
> h-bonding between O2 and [4Fe-4S] cluster) as well as looking at native
> contacts or using the closest command.
> I failed with the implicit ligand sampling tool in VMD too and I want to
> ask you if you know of any other turnaround to calculate that.
>
> Kind regards,
> Damiano Spadoni
>
>
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Received on Mon Apr 12 2021 - 10:30:02 PDT
