On Tue, May 25, 2010 at 8:06 AM, case <case.biomaps.rutgers.edu> wrote:
> On Tue, May 25, 2010, Rilei Yu wrote:
> >
> > When I installed the updated script, the error appears as follows:
> >
> > r.yu.euphoria:~/amber10/src/mmpbsa_py$ make serial
> > /bin/bash setup.sh
> > Python version 2 detected. No file conversion necessary.
> > /bin/cp MMPBSA.py *pyc /home/r.yu/amber10/bin
> > /home/r.yu/amber10/bin/nab -o mmpbsa_py_nabnmode mmpbsa_entropy.nab
>
> The new mmpbsa_py scripts are built for Amber11, not Amber10. It may be(?)
> that it is enough to get AmberTools 1.4 -- that would suffice for this
> particular step, but I'm not sure whether things in Amber11 itself are
> needed
> as well.
>
I had not tested the nab program with an old version of AmberTools, so it is
likely that AmberTools 1.4 is necessary to build the nab entropy program.
However, the only other feature that requires amber11 is energy
decomposition (until/unless a bugfix is released for amber10 that allows
decomp to work properly with imin=5).
A temporary workaround that I can think of is to change "-$(BINDIR)/nab" to
"-$(AMBERHOME)/nab" in the mmpbsa_py Makefile and make sure that AMBERHOME
points to the AmberTools-1.4 installation. This will make sure that the
correct nab is used in building mmpbsa_py_nabnmode. As long as the
installation not referred to by AMBERHOME is in the PATH, MMPBSA.py will
find the executables it needs to run.
> > nab2c failed!
> > make: [install] Error 1 (ignored)
>
> (We probably should not be ignoring make errors like this one.)
>
The reason I ignored this error was because this nab program is only
necessary for nmode entropy calculations, and I didn't want failure of this
step to halt the entire amber11 installation (as it's integrated as part of
the Amber build process). However, if memory serves, the mmpbsa_py make is
made non-fatal in the master Makefile, so perhaps we can change this to
"$(AMBERHOME)/nab" permanently...
All the best,
Jason
> ....dac
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue May 25 2010 - 06:00:21 PDT
