[AMBER] How to defining a bond between the C of the substrate and the C of the catalytic serine

From: py <py4117.163.com>
Date: Mon, 28 Feb 2011 13:34:48 +0800

Dear all,

  There I have a question about how to defining a bond between the C of the substrate and the C of the catalytic serine.
My substrate-protein complex is obtained by covalent docking,and in its docked pose, the substrate partially overlaps with
the catalytic serine. For the next work ,I need to minimize the substrate-protein complex,but they two are bonded by a
covalent bond. In my later work ,I should do the minimization as this:the substrate shoule locate in the active pocket of protein,
but without a covalent bond. So how can I define a bond between the C of the substrate and the C of the catalytic serine?

Thanks very much,

Best wishes!

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Received on Sun Feb 27 2011 - 22:34:03 PST
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