Dear Marion,
you may be interested in my research group in-house software called
AQUA-DUCT: http://www.aquaduct.pl/
AQUA-DUCT traces water molecules (or any other small molecules) within a
macromolecule of interest, which visited a particular cavity of interests.
Then it generates a visualization of the small molecules pathways and
provides the user with a set of statistics regarding each of the analysed
small molecules.
Finally, you may want to check where most of the traced molecules are
getting stuck - you can do this by computing so-called hot-spots, regions
with the highest density of the analyzed small molecules. It will also give
the information of the size and shape of the small molecules accessible
region within the macromolecule of interests, and much more!
Feel free to contact me in case of any questions or issues with the
software (we're aware it is a bit old, we're working on it!).
Best regards,
Karolina Mitusińska
pon., 8 maj 2023 o 18:56 Marion Silvestrini via AMBER <amber.ambermd.org>
napisał(a):
> Dear Amber community,
>
> I am trying to count the number of waters inside a buried pocket of a
> protein for each frame of my simulation. I have tried using the "closest"
> command on cpptraj and then apply a cut-off on the distance between the
> waters and a specific mask, but unfortunately waters inside and outside the
> pocket have the same distance to my mask.
>
> Any ideas or suggestions are appreciated!
>
> Best wishes,
> Marion.
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Received on Tue May 09 2023 - 06:30:03 PDT
