Hi,
Sorry for the late reply here. I'm really behind on answering emails.
You could potentially use the 'watershell' command and use an atom
mask that specifies only your active site. Note that 'watershell' is
OpenMP or CUDA-enabled, so you'll get results faster using OpenMP or
CUDA variants of cpptraj for that command.
-Dan
On Thu, Mar 15, 2018 at 9:22 AM, Lizelle Lubbe <LBBLIZ002.myuct.ac.za> wrote:
> Hi,
>
> I have simulated two homologous metalloproteins for 30ns and want to know how their active site accessibility to reactive oxygen species differ. The one is more prone to oxidative inactivation than the other. I’ve used caver analyst to calculate the dynamics of tunnel access and the one protein has more entry points to the catalytic zinc. Is there a way in which I can calculate the number of water molecules within the active site cavity in each frame of the simulation? I looked into GIST but the amount of detail wrt thermodynamics isn’t really needed in this case.
>
> Kind regards
>
> Lizelle Lubbe
> PhD Chemical Biology
> University of Cape Town
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-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Tue Apr 10 2018 - 06:30:04 PDT
