AMBER Archive (2008)

Subject: Re: AMBER: meet problem in adding ions and waterbox

From: Emilio Xavier Esposito (
Date: Sun Mar 30 2008 - 12:26:45 CDT

I had a similar problem with counter ions when I compile Amber on an
Intel Linux system using Portland Group (PGI) compilers. What version
of Amber do you have, how did you compile it (what compiler), and on
what OS and hardware? I recompiled Amber with g95/gcc (or was it the
Intel compilers) and the counter ions behaved as expected.

Hope this helps

On Sun, Mar 30, 2008 at 1:43 AM, Qiang Li <> wrote:
> Hi,
> 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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