Hi,
I am trying to follow the tutorial for DNA on
http://amber.scripps.edu/tutorials/basic/tutorial1/section2.htm, 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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Received on Fri Apr 18 2008 - 21:15:14 PDT
