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
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Received on Fri Oct 14 2011 - 13:30:06 PDT
