AMBER Archive (2008)

Subject: AMBER: meet problems in adding ions and waterbox

From: Qiang Li (
Date: Wed Apr 02 2008 - 00:12:31 CDT

Sorry, I wasn't meantioned my hardware and amber version last time. We are using AMD opteron, and we compile Amber 8 on Redhat Linux Enterprise 4 using Portland Group compilers. Is that a problem? We can not use g95 or gcc because some of our programs need a AMD opteron.

Below is my problem. Please help.
> 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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