[AMBER] removing few side waters (thin layer) in membranes

From: Jio M <jiomm.yahoo.com>
Date: Tue, 13 Dec 2011 03:58:22 -0800 (PST)

Dear All,

I was trying to simulate membrane in AMBER. I am able to load dry membrane in xleap without any errors. I solvate it as follows

solvatebox memb TIP3PBOX {0 0 15}

As desired and expected this gives me water up and lower part of membrane. But I provided 0 0 for the other directions few molecules of water are coming on sides (left and right side of membrane). Anyone please chime if he/she has any idea how I can remove such waters selectively or truncate side waters (few numbers though cant be removed manually in xleap)

Please some one reply for my earlier mail also

thanks and regards..

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Received on Tue Dec 13 2011 - 04:00:02 PST
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