On Fri, Nov 4, 2011 at 10:37 AM, Jan-Philip Gehrcke <jgehrcke.googlemail.com
> wrote:
> Huhu,
>
> in the PDF manual about MMPBSA Python version, it is said:
>
> > You can install MMPBSA.py using the command
> >
> > cd $AMBERHOME/src/mmpbsa_py
> > make install
> >
> > or MMPBSA.py.MPI using the command
> >
> > cd $AMBERHOME/src/mmpbsa_py
> > make parallel
>
> This should be updated to
>
> $ cd $AMBERHOME/AmberTools/mmpbsa_py
>
> Also, this "error message" really was not expressive to me:
>
> $ cd $AMBERHOME/src/mmpbsa_py
> $ make parallel
> MMPBSA.py has been moved to
> /home/bioinfp/jang/sumpf/Amber11/test/amber11/AmberTools/src
>
> Although I now know it was stupid my first impression was: hmmm.. very
> fast build process, only one file moved.
>
Hmm... it actually took me a while to realize what had happened, and I'm
the one that implemented all of those changes (via AT15_Amber11.py), which
just shows how right you are. Obviously the wording was clear to me at the
time, but the message could have been much clearer (the AT15_Amber11.py
script was rather hastily constructed).
> A cleaner solution would be:
>
> 1) removing the makefile and only keeping the README or
> 2) echoing something like "ERROR: Go to
> $AMBERHOME/AmberTools/src/mmpbs_py and invoke `make parallel` there"
>
True. Also, the message from the end of configure (urging people to "cd
../../src && make parallel") should be re-worded to suggest a parallel make
in AmberTools as well, since more and more tools are MPI there. Running
"make parallel" in AmberTools 1.5 automatically builds a parallel
MMPBSA.MPI/MMPBSA.py.MPI. I can go ahead and create a patch for this.
These issues are certainly addressed in the upcoming release of
Amber12/AmberTools, and the build process will be greatly simplified.
Thanks!
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Nov 04 2011 - 09:30:02 PDT
