I am running 64 bit ubuntu 10.04 and have had no problems with the amber
tools
including tleap.
~Levi
On Thu, May 27, 2010 at 12:20 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu May 27 2010 - 14:30:04 PDT
