[AMBER] Count water in active site

From: Lizelle Lubbe <LBBLIZ002.myuct.ac.za>
Date: Thu, 15 Mar 2018 13:22:57 +0000


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. Iíve 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 isnít really needed in this case.

Kind regards

Lizelle Lubbe
PhD Chemical Biology
University of Cape Town
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Received on Thu Mar 15 2018 - 06:30:03 PDT
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