Hello,
See my comments below:
On Sat, May 29, 2010 at 11:09 PM, Rilei Yu <yulaomao1983.yahoo.com.cn>wrote:
> Hi Dr. Jason,
>
>
> Today, I compiled 1.4 AT again, unfortunately, I still could not install
> it.This time, I did not make parallel.
>
> r.yu.euphoria:~/amber11/src/mmpbsa_py$ nab
> usage: nab [-avs] [-c] [-Dstring] [-noassert] [-nodebug] [-o file] [-v]
> file(s)
>
> 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
>
This appears to have worked. Why do you say you still could not install
it? Please note that MMPBSA.py, utils.pyc, alamdcrd.pyc, inputparse.pyc,
and mmpbsa_py_nabnmode should all be in /home/r.yu/amber11/bin, according to
your install messages, not amber10. Getting the old version to work for
your system may be complex, and there's a number of things to try (all of
which I think would be time consuming). However, based on your install
messages, I think that it actually installed (again, look in
/home/r.yu/amber11/bin).
>
> I am afraid i may cannot install this new version. The deadline is coming
> for me, so at the same time, I also want to go back to find the problem
> from the old version. When I finished MMPBSA, the output are always cleaned.
> Can you tell me how to keep them?
>
To keep all files, use keep_files=2 in your mmpbsa input file (&general
section. see the manual).
Good luck!
Jason
> I really want to check them again. Yesterday, I run one subunit with a
> ligand, it works well. But when I change it to my systerm: two adjacent
> subunits with a ligand, it fails with minimizatin steps reached 100000.
>
> Best wishes,
>
> Rilei Yu
>
> --- 10年5月29日，周六, 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29日,周六,下午9:55
>
> Hello,
>
> Did you do "make parallel" in AmberTools 1.4 before you tried to install
> MMPBSA.py? This is a fairly fine point, but MMPBSA.py should be made with a
> serial version of nab. When I built mmpbsa_entropy.nab with an MPI-enabled
> nab, it compiled just fine, but it conflicted with the MPI_WORLD of
> MMPBSA.py.MPI, but yours doesn't even appear to be compiling properly.
>
> Try re-compiling AmberTools 1.4, but don't make parallel at the end. Then
> try to build MMPBSA.py.
>
> On another note, /home/r.yu is your directory, so you typically don't need
> to use sudo (this is only for /usr/local/ directory). You may have to use
> sudo to get rid of some links you created (i.e. nab link in
> /home/r.yu/amber10/bin/nab), but in general sudo is not needed here.
>
> Good luck!
> Jason
>
> --
> Jason Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
>
> On May 29, 2010, at 7:21 AM, Rilei Yu <yulaomao1983.yahoo.com.cn> wrote:
>
> > Dear amber users,
> >
> > Very thanks for your former suggestion.
> > Tonight, I tried to install mmpbsa.py based on your suggestions.
> > 1) put the path in the .bashrc
> > export AMBERHOME=/home/r.yu/amber11
> > export PATH=$AMBERHOME/bin\:/home/r.yu/amber10/bin\:$PATH
> > 2)
> > sudo mv /home/r.yu/amber10/bin/nab /home/r.yu/amber10/bin/nab-1.2
> > sudo ln -s /home/r.yu/amber11/bin/nab /home/r.yu/amber10/bin
> >
> >
> > 3)
> > cd $AMBERHOME/src/mmpbsa_py
> >
> > make serial
> >
> > make parallel
> >
> > r.yu.euphoria:~/amber11/src/mmpbsa_py$ 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
> > /home/r.yu/amber11/lib/libnab.a(sff.o): In function `mme_timer':
> > sff.c:(.text+0x2b40): undefined reference to `lam_mpi_comm_world'
> > sff.c:(.text+0x2b4e): undefined reference to `lam_mpi_max'
> > sff.c:(.text+0x2b53): undefined reference to `lam_mpi_double'
> > sff.c:(.text+0x2bda): undefined reference to `MPI_Allreduce'
> > /home/r.yu/amber11/lib/libnab.a(sff.o): In function `mpierror':
> > sff.c:(.text+0x86c6): undefined reference to `lam_mpi_comm_world'
> > sff.c:(.text+0x86cc): undefined reference to `lam_mpi_min'
> > sff.c:(.text+0x86df): undefined reference to `lam_mpi_int'
> > sff.c:(.text+0x86e9): undefined reference to `MPI_Allreduce'
> > sff.c:(.text+0x8701): undefined reference to `MPI_Finalize'
> > /home/r.yu/amber11/lib/libnab.a(sff.o): In function `mpiinit':
> > sff.c:(.text+0xca2c): undefined reference to `MPI_Init'
> > sff.c:(.text+0xca4d): undefined reference to `lam_mpi_comm_world'
> > sff.c:(.text+0xca52): undefined reference to `MPI_Comm_rank'
> > sff.c:(.text+0xca62): undefined reference to `lam_mpi_comm_world'
> > sff.c:(.text+0xca67): undefined reference to `MPI_Comm_size'
> >
> > So I went back to re-install the tool.1.4 again, and found the same
> problem. Can you give me more suggestions.
> >
> > I am really appreciated for your suggestions again!
> > Best wishes,
> >
> >
> > Rilei Yu
> >
> > --- 10年5月29日，周六, 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29日,周六,上午4:38
> >
> > On Fri, May 28, 2010 at 1:20 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >
> >>> 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.
> >>
> >> It doesn't work this way - your environment has only one AMBERHOME
> >> variable, it is not like a path where directories are indexed
> >> sequentially.
> >>
> >
> > Yes. One at a time. To install amber10, though, AMBERHOME needs to point
> to
> > /usr/local/amber10 temporarily (while the install is taking place). Then
> it
> > should point to /usr/local/amber11 to install AmberTools 1.4, and it
> should
> > remain pointing to /usr/local/amber11 after it's done (since AmberTools
> > makes the most use of AMBERHOME; indeed probably the only use of it).
> > However, in order for MMPBSA.py to operate successfully, both
> > /usr/local/amber10/bin and /usr/local/amber11/bin must be in the PATH,
> with
> > /usr/local/amber11 coming first so AmberTools-1.4 binaries are used
> before
> > AmberTools-1.2 that reside in /usr/local/amber10. This is what Bill
> meant,
> > I believe. (Though defining AMBERHOME a second time in the .bashrc does
> > overwrite the first definition).
> >
> > For installing MMPBSA.py, though, you should probably create a symbolic
> link
> > from nab in /usr/local/amber11/bin to the directory
> /usr/local/amber10/bin
> > in order to build the nmode program with the proper nab compiler. You
> can
> > do this as follows:
> >
> > sudo mv /usr/local/amber10/bin/nab /usr/local/amber10/bin/nab-1.2
> > sudo ln -s /usr/local/amber11/bin/nab /usr/local/amber10/bin
> >
> > I used sudo because typically users don't have write permissions in
> > /usr/local, but if you changed the ownership of /usr/local/amber10 and
> 11,
> > then you don't need the sudo (but if you don't need the sudo, you
> generally
> > know you don't...)
> >
> > What this does is to move nab from AT 1.2 "out of the way" so that a soft
> > link can be put in /usr/local/amber11/bin, so that MMPBSA.py installation
> > will use that.
> >
> > Ideally what should be in your .bashrc should look something like this:
> >
> > export AMBERHOME=/usr/local/amber11
> > export PATH=$AMBERHOME/bin\:/usr/local/amber10/bin\:$PATH
> >
> > Hope this helps,
> > Jason
> >
> >
> >> Bill
> >>
> >> _______________________________________________
> >> 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
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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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 Sat May 29 2010 - 21:30:03 PDT
