Sorry, it is not released in the tarball, but is linked to in the MMPBSA.py
online tutorial in multiple sections. Regardless, I have attached the manual
in this e-mail as well.
-Bill
On Sun, May 30, 2010 at 8:26 PM, Rilei Yu <yulaomao1983.yahoo.com.cn> wrote:
> Hi amber users,
>
> I checked it, it was Python 2.4.3. So this may be this problem. What is
> more, can you send me a pdf version of the new manual? In fact, I did not
> find it is in the tar box file (test and mmpbsa). May be I failed to find
> the 3th tar file?
>
> Very thanks,
>
> Rilei Yu
>
> --- 10年5月30日，周日, 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30日,周日,下午9:32
>
> Hello Rilei,
>
> I just downloaded the source code from the website, installed it, and
> tested
> it, and it worked just fine.
>
> I have a couple guesses as to what your problem may be. First: What
> version
> of python do you have? Find out with the command
>
> python -V
>
> I'm guessing you have something older than python 2.5 (these older versions
> do not support some of the syntax used in MMPBSA.py, so you will need to
> download a more recent version of python). To be safe, make sure you have
> some version of Python 2.6 (2.6.5 is the latest stable version in Python2
> available right now).
>
> Second: Did you erase your old version of MMPBSA.py? Try and make sure that
> all old versions of MMPBSA.py are uninstalled. (make uninstall in the old
> mmpbsa_py directories).
>
> Good luck!
> Jason
>
> On Sun, May 30, 2010 at 1:28 AM, Rilei Yu <yulaomao1983.yahoo.com.cn>
> wrote:
>
> > Hi, Dr Jason,
> >
> > Here is the information:
> > r.yu.euphoria:~$ $AMBERHOME/bin/MMPBSA.py
> > Traceback (most recent call last):
> > File "/home/r.yu/amber11/bin/MMPBSA.py", line 629, in ?
> > utils.gbmdin(INPUT) # create our own
> > File "/home/ryu/amber11/src/mmpbsa_py/utils.py", line 329, in gbmdin
> > mdin.write(
> > AttributeError: 'str' object has no attribute 'format'
> >
> > r.yu.euphoria:~/amber11/test/mmpbsa_py$ 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
> > ./Run.ALA: line 45: ../../dacdif: No such file or directory
> > 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 directory
> >
> > MMPBSA.py -i mmpbsa.in -sp complex_solvated.prmtop -cp complex.prmtop
> -rp
> > re.prmtop -lp lig.prmtop -y complex_md0.mdcrd
> > Traceback (most recent call last):
> > File "/home/r.yu/amber11/bin/MMPBSA.py", line 477, in ?
> > INPUT[0] = inputparse.InputParse(inputfile_name, INPUT, warnings)
> > File "/home/ryu/amber11/src/mmpbsa_py/inputparse.py", line 129, in
> > InputParse
> > print >> sys.stderr, 'Warning: Input error! "{0}" is an invalid
> > option.'.format(ychk)
> > AttributeError: 'str' object has no attribute 'format'
> >
> > By the way, in the new version, is there any change on the command line
> and
> > input file?
> >
> > Waiting for your response.
> > Thanks again!
> >
> > --- 10年5月30日，周日, 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30日,周日,下午12:00
> >
> > 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
> > >
> > > _______________________________________________
> > > 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
> > >
> >
> >
> >
> > --
> > 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
> >
>
>
>
> --
> 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
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun May 30 2010 - 18:00:03 PDT
