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-- Jason Swails Quantum Theory Project, University of Florida Ph.D. Graduate Student 352-392-4032 On May 30, 2010, at 9:59 PM, Rilei Yu <yulaomao1983.yahoo.com.cn> wrote: > Very thanks for your help again. > Now, I am waiting for the manager to install python2.6 in the system of our institute. Maybe I need wait for long time this time. By the way why do you make the program so complicated this time? Last time. we just pasted it in the amber package, that was ok. > > Another question is still about the old version. The receptor of my protein has two subunits, and the binding site is in the middle of the two subunits. Yesterday, I deleted one subunit but kept the ligand still. To my surprise, it works now (for entropy calculation). Unfortunately, when I went back and use the two subunits and my ligand, it did not work again. I really doubt it would be the problem of the converge. > > Rilei Yu > > --- 10年5月31日，周一, 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31日,周一,上午8:50 > > Hello, > > Sorry, I do realize that it is pretty hard to find, but it is linked to several times in the tutorial itself. The URL to obtain it is http://ambermd.org/tutorials/advanced/tutorial3/py_script/files/MMPBSA_Python_Manual.pdf > > Good luck! > Jason > > -- > 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 > > > > > _______________________________________________ > 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/amberReceived on Sun May 30 2010 - 21:00:03 PDT