Custom Search
--
Jason Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
On 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun May 30 2010 - 18:00:05 PDT