AMBER Archive (2008)

Subject: AMBER: meet problem in adding ions and waterbox

From: Qiang Li (
Date: Sun Mar 30 2008 - 00:43:54 CDT

I am trying to follow the tutorial for DNA on, and I met two big problems.
(1) I say addions model Na+ 0 in xleap, and I got exactly the same output messages as the tutorial said. However, when I open it in xleap editor, all the Na+ were arranged in a line and they were all on the top of the DNA. I tried many times and I don't know how to solve this problem.

(2) I also try to add a waterbox to DNA before I add ions. I say solvatebox model TIP3PBOX 8.0, and I find that the long axis of waterbox is not along the long axis of the DNA. Thus, it looks like half of the DNA is outside the waterbox.

Thus, I tried solvateoct model2 TIP3PBOX 8.0. However, I still met the same problem. I wonder how can you put the whole DNA into the waterbox. Is there something wrong with my computer. It seams it always adds ions/waters to the wrong place.

Please help!

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