[AMBER] Question about Empirical Valence Bond(EVB) simulation

From: 没关系 <yangzhilin0723.qq.com>
Date: Wed, 4 Jan 2017 10:21:21 +0800

Dear Amber users,

I want to do an EVB simulation of the hydrogen transfer step of an enzymatic reaction. With help of the Amber Manual,I have successfully ran an EVB simulation including two molecules and obtained a PMF curve.
However, I do not know how to do an EVB simulation including the whole protein environment(the two molecules in the active center are used in EVB calculation, and the protein acts as the environment in the MD simulation). Does Amber can do so ? if it can do, how to identify the EVB region and the protein environment?

Thanks in advance for any help!
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Received on Tue Jan 03 2017 - 18:30:02 PST
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