Thank you both for suggestions.
I downloaded AQUADUCT and I was going to give it a try as it seems to be a straightforward calculation.
I'll compare it with the new hbond command Dan just provided.
Speaking of new implementations, AQUADUCT could be useful in cpptraj as well as a protein tunnel calculation software (e.g. CAVER) to increase structural investigations in proteins.
Damiano
________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Tuesday, April 13, 2021 2:48 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] How to track oxygen molecules in MD
Hi,
On Mon, Apr 12, 2021 at 12:51 PM Damiano Spadoni
<Damiano.Spadoni.nottingham.ac.uk> wrote:
> 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.
You don't actually need hydrogen bonds to form; you can just make it
so that there is no angle criterion (by specifying 'angle -1'), only a
distance criterion. You can also make tracking the oxygen non-specific
by using the solventdonor/solventacceptor keywords and treating them
as "solvent", e.g. 'hbond HB-Oxygen angle -1 out nhb.agr avgout
oxygen_avg.dat solventacceptor <oxygen mask> solventdonor <oxygen
mask>'.
However, the code recommended by Karolina may be closer to what you
need. .Karolina any chance you want to implement AQUA-DUCT in cpptraj?
:-)
-Dan
> 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 Tue Apr 13 2021 - 07:30:02 PDT
