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
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Received on Fri Oct 14 2011 - 16:30:03 PDT
