[AMBER] conserved water in MMPBSA

From: Albert <mailmd2011.gmail.com>
Date: Fri, 12 Jun 2015 15:03:15 +0200


I've got a question about conserved water in MMPBSA calculation.
Sometimes in the protein/ligand system there are 1-2 conserved water
mediating the interaction between protein and ligand, and I am just
wondering shall we keep those water molecules "explicitly" during MMPBSA
calculation? In this case, we treat them as a part of protein instead of
strip them off from the calculation system.

Does anybody have any idea is it necessary to do so? If we do this, will
this increase the accuracy of our calculation?

thx a lot


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Received on Fri Jun 12 2015 - 06:30:07 PDT
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