Sorry it did not replace it. But by untar the AmberTool1.5 on top of amber11
will not let the initial steps of installation work.
On Fri, Oct 14, 2011 at 6:59 PM, Jason Swails <jason.swails.gmail.com>wrote:
> It shouldn't replace the directory -- it should just extract into the same
> one (if it replaced it then unpacking Amber11 + AmberTools 1.4/5 would be a
> much bigger pain). It should set right on top of the old AmberTools in
> your
> amber11 directory and replace the relevant source files common to both.
>
> HTH,
> Jason
>
> On Fri, Oct 14, 2011 at 4:25 PM, Mo Chen <mc842.cornell.edu> wrote:
>
> > Hi Jason
> > Thank you very much! I have tried to extract an AmberToos 1.5 on top of
> my
> > amber11 extract, but it did not merge and instead it substituted the
> > amber11. I will try to get a hold of the Amber11.tar.bz2 and do the
> > installation again.
> >
> > Best,
> > Mo
> >
> > On Fri, Oct 14, 2011 at 3:48 PM, Jason Swails <jason.swails.gmail.com
> > >wrote:
> >
> > > On Fri, Oct 14, 2011 at 2:20 PM, Mo Chen <mc842.cornell.edu> wrote:
> > >
> > > > Hi Jason,
> > > > My replies to your comments are as below. Thank you very much!
> > > >
> > > > On Fri, Oct 14, 2011 at 6:20 AM, Jason Swails <
> jason.swails.gmail.com
> > > > >wrote:
> > > >
> > > > > On Thu, Oct 13, 2011 at 11:21 PM, Mo Chen <mc842.cornell.edu>
> wrote:
> > > > >
> > > > > > Dear Amber users/developers,
> > > > > > I have a problem installing parallel version of amber in my
> > machine.
> > > I
> > > > > was
> > > > > > trying to compile amber using intel compiler and mpich2 library.
> > And
> > > > my
> > > > > > procedure was shown as below:
> > > > > >
> > > > > > chen.sugar9:~$ tar xzvf amber11-06-26-2011.tgz
> > > > > >
> > > > >
> > > > > Does this tarball contain Amber11 + AmberTools 1.5?
> > > > >
> > > > >
> > > > > > chen.sugar9:~$ cd amber11
> > > > > > chen.sugar9:~$ echo $SHELL
> > > > > > /bin/bash
> > > > > > chen.sugar9:~$ echo "export AMBERHOME=$PWD" >> ~/.bashrc
> > > > > > chen.sugar9:~$ echo "export PATH=$PATH:$AMBERHOME/bin" >>
> > ~/.bashrc
> > > > > > chen.sugar9:~$ source ~/.bashrc
> > > > > > chen.sugar9:~$ wget
> > > > > http://ambermd.org/bugfixes/AmberTools/1.5/bugfix.all
> > > > > > chen.sugar9:~$ patch -p0 -N < bugfix.all
> > > > > > chen.sugar9:~$ rm bugfix.all
> > > > > > chen.sugar9:~$ cd AmberTools/src/
> > > > > > chen.sugar9:~/AmberTools/src$ ./configure intel
> > > > > > chen.sugar9:~/amber11/AmberTools/src$ make install
> > > > > > chen.sugar9:~/amber11/AmberTools/src$ cd
> > > > > > chen.sugar9:~$ cd $AMBERHOME
> > > > > > chen.sugar9:~/amber11$ wget
> > > > > > http://ambermd.org/bugfixes/11.0/bugfix.1to17.tar.bz2
> > > > > > chen.sugar9:~/amber11$ wget
> > > > > > http://ambermd.org/bugfixes/11.0/apply_bugfix.x
> > > > > > chen.sugar9:~/amber11$ ./apply_bugfix.x bugfix.1to17.tar.bz2 (
> > this
> > > > > does
> > > > > > not work)
> > > > > >
> > > > >
> > > > > This is way too vague. What do you mean it didn't work? What
> errors
> > > did
> > > > > you get? Until this step works, there's really little point in
> going
> > > > > further with the Amber 11 installation.
> > > > >
> > > >
> > > > I will put the path in front of the tar file, as said by Niel.
> > Hopefully
> > > it
> > > > will work.
> > > >
> > >
> > > It will not fix the error with RISM you were reporting.
> > >
> > >
> > > >
> > > > >
> > > > >
> > > > > > chen.sugar9:~/amber11$ cd AmberTools/src/
> > > > > > chen.sugar9:~/AmberTools/src$ ./configure intel
> > > > > > chen.sugar9:~/amber11/AmberTools/src$ cd $AMBERHOME
> > > > > >
> > > > >
> > > > > After this step you should be running the AT15_Amber11.py script if
> > you
> > > > are
> > > > > building AmberTools 1.5 + Amber11. The instructions are stated at
> > the
> > > > end
> > > > > of the configure script.
> > > > >
> > > > >
> > > > I did not see AT15_Amber11.py in $AMBERHOME directory.
> > >
> > >
> > > Then it's not AmberTools 1.5. It must be AmberTools 1.4 (unless the
> > person
> > > that gave you the tarball did some weird surgeries and pieced together
> > code
> > > from different versions, which isn't likely).
> > >
> > >
> > > > I was told that the
> > > > amber11-06-26-2011.tgz file contains both amber11 and AmberTools.
> > >
> > >
> > > But not the proper version of AmberTools.
> > >
> > >
> > > > And after
> > > > I did the patch -p0 -N < bugfix.all, there was AT15_amber11.py.orig
> > and
> > > > AT15_amber11.py.rej files. So I thought it had been run
> automatically.
> > > >
> > >
> > > Nope. These files were generated because the AmberTools 1.5 bugfix.all
> > > patches AT15_Amber11.py, and so it generates an original file (blank
> > file)
> > > and a rejected patch file (.rej) from the failed patch attempt.
> > >
> > > My suggestion is to get ahold of the Amber11.tar.bz2 distributed from
> the
> > > Amber website and combine that with an AmberTools 1.5 download you can
> > get
> > > for free from http://ambermd.org and follow the instructions from
> there.
> > >
> > > You can *try* to just extract an AmberTools 1.5 source tree on top of
> > your
> > > amber11 extract and build from there, but since I don't know what state
> > the
> > > source code was given to you in, I can't guarantee that this will work.
> > >
> > > HTH,
> > > Jason
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Candidate
> > > 352-392-4032
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Oct 14 2011 - 17:00:02 PDT
