Hi,
On Tue, Dec 13, 2022 at 3:27 PM Damiano Spadoni via AMBER
<amber.ambermd.org> wrote:
> On a different task, would it make sense to use the RDF function to look for the number of water molecules that get in the different active sites, i. e. the RDF of wat mols around the metal cofactor in the active site? Or the Watershell command is more indicated for the study?
They're fundamentally very similar - watershell is essentially just 2
unnormalized bins of a RDF histogram (the RDF of course is just a
molecule count histogram normalized by expected molecule density over
slices of increasing volume). The RDF will provide you more
information as long as it's properly normalized (which it
approximately is for water by default). Hope this helps,
-Dan
>
> Kind regards,
> Damiano
> ________________________________
> Da: Damiano Spadoni <ezads12.exmail.nottingham.ac.uk>
> Inviato: martedì 8 novembre 2022 13:35
> A: amber.ambermd.org <amber.ambermd.org>
> Oggetto: Reimaging issues
>
> Hi AMBERists,
>
> I am having issues in reimaging the MD simulations of a Protein in an orthorombic box of water. I want to check the permeability of the catalytic pocket through the homodimeric structure of the protein, if a different number of water molecules get into the active site of each monomer. To do this I thought to calculate the coordination number of the metal centre in the active site vs. water molecules. You might suggest a different strategy for doing this - am open to suggestions, of course.
> My issue comes from the attempts of reimaging the trajectories as I thought water molecules should be included to measure how many of those get into the different pockets. The output coming from my cpptraj script seems to have the water box centred but not the protein, the protein always looks shifted from the centre of the box and there are "cavities" in the water box. My script looks like this:
>
> parm Protein.prmtop
> trajin Protein_md10ns.mdcrd 0 last 50
> unwrap :1-1640 #the protein is 1640 amino acid long
> image origin center :1-1640 familiar
> center :1-1640 mass origin
> autoimage
> trajout Reimaged_trajectories.nc netcdf
>
> Kind regards,
> Damiano
>
>
>
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Received on Tue Jan 17 2023 - 05:00:02 PST
