AMBER: solvation issues

From: Eddie Men <>
Date: Wed, 26 Sep 2007 17:19:47 -0600

Dear Amber users.

Here is the task I have at hand. I want to model the active site of a
protein with explicit water molecules
(used solvateCap), and the non active site of the protein will be born
model (igb=12).

I would like to know if it is possible to make constant pH simulations
with such a system,
however I wonder how such formalism is implemented. If my water cap is
neutral, how does it
"feel" the effects of changing the pH in the surroundings?. If it
doesn't should I instead place
OH explicit ions inside the cap region AND THEN build the cap?.

Also, about the cap, does it keep the same number of solvant molecules
during the simulation or
is it a subsystem with constant volume?. I am of course using quantum
regions smaller than the
cap raddi

I thank you in advance for your feedback

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Received on Sun Sep 30 2007 - 06:07:17 PDT
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