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
>
>
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> 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
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Received on Fri May 28 2010 - 00:00:07 PDT
