When you install AmberTools 1.4 you will not need to uninstall AmberTools
1.2 or Amber 10. Instead, just place the path for Amber 11 (export
AMBERHOME=/usr/local/amber11) before defining the path for Amber 10
(AMBERHOME=/usr/local/amber10) in your .bashrc file. This will set up your
environment such that the computer will look for the executable files in
Amber 11 *before* the executable files in Amber 10, which is what you want.
You want the computer to use all the AmberTools 1.4 executables and really
only have to use the Amber 10 folder for sander or pmemd.
The tests obviously did not pass since the correct files were never made. If
you change directories into the individual test folders, are there any new
files there that were made? If the calculation had an error there should be
files in there that will have error messages in them. You might want to try
to change directories into one of the test directories and executing the
Run.sh file (./Run.sh) so that you can see the progress of the calculation
printed to the screen and any errors that might help.
Also, I assume you set DO_PARALLEL before the test, since you go the error:
Error: You must install the mpi4py package to use MMPBSA.py.MPI!
If you want to run the MPI version of MMPBSA.py, you will need to download
and install the mpi4py package. There is a link and instructions for
download and installation of this package on the MMPBSA.py tutorial website
(
http://ambermd.org/tutorials/advanced/tutorial3/py_script/compile.htm).
I hope this helped.
-Bill
On Fri, May 28, 2010 at 2:21 AM, Rilei Yu <yulaomao1983.yahoo.com.cn> wrote:
> Dear amber users,
>
> Recently, I try to install the mmpbsa.py, the updated one, you really give
> me some help, but I still cannot install until now. I really have poor
> knowledge on the linux, recently I am borrowing books to improve it.
>
> Here I still have several questions:
> When I install the amber tools 1.4, should I uninstalled the tools 1.2
> first? Should I re-install amber 10?
>
> Now, I am a bit of confused to install amber10 with tools 1.4. Can you give
> me more suggestions? (For instance, in the tools installing process, I will
> set export AMBERHOME=/usr/local/amber11. But in the amber10 install, I set
> AMBERHOME=/usr/local/amber10. There will be one varibles for two programs.
> Will the computer be confused? )
>
> Today, I just installed amber-tools 1.4, while I did not re-install
> amber10, when i type test there are some errors
>
> r.yu.euphoria:~/amber11/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/amber11/bin
> /home/r.yu/amber11/bin/nab -o mmpbsa_py_nabnmode mmpbsa_entropy.nab
> /bin/mv mmpbsa_py_nabnmode /home/r.yu/amber11/bin
> r.yu.euphoria:~/amber11/src/mmpbsa_py$ make parallel
> /bin/bash setup.sh
> Python version 2 detected. No file conversion necessary.
> /bin/cp MMPBSA.py.MPI *pyc /home/r.yu/amber11/bin
>
>
> r.yu.euphoria:~/amber11/test/mmpbsa_py$ make test
> cd 01_Generalized_Born && ./Run.GB
> ./Run.GB: line 37: ../../dacdif: No such file or directory
> cd 02_Poisson_Boltzmann && ./Run.PB
> ./Run.PB: line 37: ../../dacdif: No such file or directory
> cd 03_Alanine_Scanning && ./Run.ALA
> ./Run.ALA: line 42: ../../dacdif: No such file or directory
> Mutant mdcrd can only be checked in serial
> Error: You must install the mpi4py package to use MMPBSA.py.MPI!
> cd 04_Per_Residue_Decomp && ./Run.PerRes
> ./Run.PerRes: line 40: ../../dacdif: No such file or directory
> ./Run.PerRes: line 41: ../../dacdif: No such file or directory
> cd 05_Pairwise_Decomp && ./Run.Pairwise
> ./Run.Pairwise: line 40: ../../dacdif: No such file or directory
> ./Run.Pairwise: line 41: ../../dacdif: No such file or directory
> cd 06_NAB_Nmode && ./Run.nmode
> ./Run.nmode: line 34: ../../dacdif: No such file or directory
> cd 07_Comprehensive && ./Run.comprehensive
> ./Run.comprehensive: line 71: ../../dacdif: No such file or directory
> ./Run.comprehensive: line 72: ../../dacdif: No such file or directory
> ./Run.comprehensive: line 73: ../../dacdif: No such file or director
>
> Very thanks for your suggestion!
> Rilei Yu
>
> --- 10年5月25日，周二, Jason Swails <jason.swails.gmail.com> 写道：
>
> 发件人: Jason Swails <jason.swails.gmail.com>
> 主题: Re: [AMBER] MMPBSA.py update install problem
> 收件人: "AMBER Mailing List" <amber.ambermd.org>
> 日期: 2010年5月25日,周二,下午8:21
>
> 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
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Fri May 28 2010 - 04:30:04 PDT
