Re: [AMBER] Installing amber10 on ubunta, some hints please.

From: Paul S. Nerenberg <>
Date: Wed, 9 Jun 2010 08:55:22 -0700

Hi Cat,

Assuming you've done everything that Jason has suggested, see my
replies below...

> Dear Amber administrators,
> I am new to install amber10 on unbunta.
> I wonder if I have to do "./configure gcc" and do "make -f
> Makefile_at", and then do another compilation with gfortran again
> with the following commands lines "./configure gfortran" and do
> "make -f clean Makefile_at" again to compile all the units in Amber
> tools?
No, you only have to do "./configure gcc" and "make -f Makefile_at".
At this point, I would advise doing a "make -f Makefile_at clean"
*before* you start trying to build anything again just to be sure that
you are rid of any leftovers from your previous build attempts.

> I also wonder if we should "tar xvfj AmberTools.tar.bz2" under root
> or sudo command.
This depends on what directory you want to install AmberTools in. If
you just want to put it in /home/your_username/amber10, then you don't
need to do this. If you want to put it in /usr/local/amber10, then
you most likely will have to do it with sudo. Personally, I just
build things in my home directory, not in /usr/local.

> I know X11 library is needed to install amber on red hat linux. Do
> i need to define any library location in .bashrc when I do the
> installation on ubunta?
Not true. You can always build AmberTools without X11 support. In
fact, unless you really need the X11 support, you might consider
building AT without it. This can be done with "./configure -noX11 gcc
". I'd recommend trying to build things first this way just to see if
you get any further than you have previously...

> Attached is the ./config.h file I created with ./configure gcc
> only. However, I tried many times, the sleap tests still have error
> that "find not found" (all other tests are OK). I am wondering if I
> have not compile the sleap properly with the right compiler or I
> should not extract the files as a root or I did not define the
> necessary library correctly.
Let's see what you get after you try again...



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Received on Wed Jun 09 2010 - 09:00:10 PDT
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