[AMBER] problem during TMD simulation

From: Dachuan Guo <dcguo.hust.gmail.com>
Date: Mon, 13 Dec 2010 16:45:10 +0800

Amber users,

    I have two protein structures A/B with the same sequence. I want
to use TMD to simulate the process from A to B. When I used
"solvateoct *** TIP3PBOX 9.0", there were different number of residues
added to system A and B. TMD can't run without the same number of
atoms.
How could I add the same number of water into the two protein systems?

regards,
Dachuan Guo

-- 
Dachuan Guo
------------------------------------------------------------------
Biomolecular Physics and Simulation Group, Department of Physics,
Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
Tel：86-27-87558335-606
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Chinese Version:
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郭大川
华中科技大学物理学院  生物分子物理与模拟研究组
湖北省武汉市洪山区珞瑜路1037号
邮编：430074
电话：86-27-87558335-606
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Received on Mon Dec 13 2010 - 01:00:04 PST