Hello,
On Thu, May 27, 2010 at 2:36 PM, David Dubins <d.dubins.utoronto.ca> wrote:
> Hi everyone,
>
> I thought I'd upload this install script for Ubuntu 10.04 for AmberTools
> 1.4, because it worked. This will be obvious to most of you, but useful for
> newbies like me. Please note that I installed Ubuntu 32 bit version (the 64
> bit version resulted in segmentation faults when loading forcefields in
> xleap and tleap).
>
Just be aware of the limitations of using a 32-bit OS over a 64-bit OS.
Note that sleap does not suffer from these issues, and I believe that a
bugfix for this issue is close at hand. I would probably use the 64-bit
version and use sleap (since it's newer and actively developed), and wait
for bugfixes to come out.
>
> 1) Download AmberTools version 1.4 and extract it into your user directory
> (replace "user" in the below instructions with your user directory name)
>
> 2) Open up a terminal window:
> Click Applications --> Accessories --> Terminal
>
> 3) In the terminal window, add the following line to .profile by typing:
>
> cd ~
> pico .profile
>
> (on the bottom of the file, type:)
>
> export AMBERHOME=/home/user/amber11
> PATH="$HOME/amber11/exe:$PATH"
>
> (Ctrl-X to exit)
>
> source .profile
>
> Now add the following line to .bashrc:
>
> pico .bashrc
>
> (on the bottom of the file, type:)
> AMBERHOME=$HOME/amber11
> export AMBERHOME
>
> MPI_HOME=/
> export MPI_HOME
>
> (Ctrl-X to exit)
>
> source .bashrc
>
> 4) Download AmberTools bug fixes:
> http://ambermd.org/bugfixesat.html
>
> Copy bugfix.all into the amber11 directory.
>
> 5) In a terminal window, type:
> cd ~/amber11
> patch -p0 -N < bugfix.all
>
> sudo apt-get install bison
> sudo apt-get install csh
> sudo apt-get install flex
> sudo apt-get install gfortran
> sudo apt-get install g++
> sudo apt-get install xorg-dev
>
> cd ~/amber11/AmberTools/src
>
> ./configure gnu
> make install
>
> cd ../test
> make test
>
> That's it! Best,
> -Dave
>
> PS: I noticed that GROMACS comes already installed in Ubuntu (no sudo
> apt-get even required!). Maybe AmberTools can hop on the bandwagon?
>
I'd be surprised if gromacs was actually on the install disc (at least the
downloadable CD, the DVD maybe). Ubuntu continues to embrace the CD (after
most other distros have gone the DVD route), so they have to cut a lot of
corners to keep their distro small enough to fit on 700 MB (which is why
there's a long list of packages that need to be installed before amber is
used for ubuntu but not other packages). It would be more likely that
AmberTools would be available through aptitude if anyone actually goes
through the effort of building packages for the ubuntu repos and putting
them in there. However, Amber itself is not open source, and the structure
of the AmberTools/Amber package does not very much lend itself to
installation via aptitude (and emerge, yum, port, etc.), so I would not be
surprised if this development was very long in coming.
>
> ------------------------------------------------------
> David Dubins, Ph.D., B.Eng.
> Instructor and Laboratory Coordinator
> Leslie Dan Faculty of Pharmacy
> University of Toronto
> 144 College Street Toronto, Ontario M5S 3M2
> Telephone: 416-946-3840
> Mobile: 647-891-8685
> d.dubins.utoronto.ca
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu May 27 2010 - 12:30:05 PDT
