AMBER Archive (2005)

Subject: AMBER: The “crystallographic” waters should be retained or deleted?

From: haixiao jin (jinhx952_at_gmail.com)
Date: Wed Aug 10 2005 - 07:35:34 CDT

Dear Amber users,
The crystallographic water molecules were discarded in some papers,
while the crystallographic water molecules were keep in other papers.
Opinions differ on this matter. But in most case, how to deal with
those crystallographic is not mentioned.
How the result of MD will be affected in the different ways? In my
opinion, those crystallographic water molecules should be remained,
because they may from hydrogen-bonded networks with protein. Is it
right?
Many paper mentioned that water molecules whose oxygen atoms were less
than 2.45Å from any protein heavy atom were deleted. Is the distance
less than hydrogen bond?
I am confused with it. Please give me a hand, thank you!
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