Defining PYTHONPATH in the job script should be able to help you define the
correct version of python inside the script.
-Bill
On Wed, Jun 2, 2010 at 4:53 AM, Rilei Yu <yulaomao1983.yahoo.com.cn> wrote:
> Thanks for you suggestion. Before I used python 2.4, but for the installing
> of the new mmpbsa-script, I installed python 2.6.5. Can you give me details
> on how to change it?
>
> I am appreciated for your help again!
>
> Rilei Yu
>
> --- 10年6月2日，周三, Dwight McGee <dwight.mcgee.gmail.com> 写道：
>
> 发件人: Dwight McGee <dwight.mcgee.gmail.com>
> 主题: Re: [AMBER] MMPBSA.py update install problem
> 收件人: "AMBER Mailing List" <amber.ambermd.org>
> 日期: 2010年6月2日,周三,下午4:14
>
> Bad magic number error: Make sure that you are consistent and using same
> version of python used to create the .pyc files.. Be certain to specify
> your
> python version in your job script if it differs from the version on your
> cluster.
>
> On Wed, Jun 2, 2010 at 2:18 AM, Rilei Yu <yulaomao1983.yahoo.com.cn>
> wrote:
>
> > Dear Dr. Jason,
> > Very thanks for your so detailed explanation on these two approaches.
> > After I installed the script, I want to run it in the cluster. When I
> tried
> > to use "qsub script" commmand, it still cannot work. But I am sure we
> have
> > installed it, because it works when I used command line on the shell
> > directly.
> >
> > You know, using command line is really bad, as other people also use the
> > cluster, what is worse, I cannot submit may jobs a one time. I even
> change
> > the env in the script but it nevers works.
> > My script is:
> > Before I installed it my script was:
> > #!/bin/csh
> >
> > #PBS -q normal
> >
> > #PBS -N RileiJob
> >
> > #PBS -l ncpus=1,vmem=3000mb,walltime=216000
> >
> > cd $PBS_O_WORKDIR
> >
> > setenv PATH
> >
> >
> /opt/csm/bin:/bin:/usr/bin:/usr/X11R6/bin:/opt/bin:/opt/pathscale/bin:/opt/bin:/opt/lam/bin/:/home/ryu/bin/:/home/ryu/amber10/bin/
> >
> > lamboot
> > It worked well when I used amber 10 for the old mmpbsa version.
> > As I installed the new script, I also changed it to:
> > #!/bin/csh
> > #PBS -q normal
> > #PBS -N RileiJob
> > #PBS -l ncpus=1,vmem=3000mb,walltime=216000
> > cd $PBS_O_WORKDIR
> > setenv PATH
> >
> /opt/csm/bin:/bin:/usr/bin:/usr/X11R6/bin:/opt/bin:/opt/pathscale/bin:/opt/bin:/opt/lam/bin/:/home/ryu/bin/:/home/ryu/amber11/bin/:/home/ryu/amber10/bin/
> > lamboot
> > MMPBSA.py -O -i mmpbsa.in -sp complex_solvated.prmtop -cp complex.prmtop
> > -rp receptor.prmtop -lp ligand.prmtop -y complex_solvated.mdcrd -o
> > mmpbsa.dat
> > However, I tried many times, it still did not work.
> > The errors are:
> > Traceback (most recent call last):
> > File "/home/ryu/amber11/bin/MMPBSA.py", line 43, in ?
> > import inputparse, utils, alamdcrd # (2)
> > ImportError: Bad magic number in /home/ryu/amber11/bin/inputparse.pyc
> >
> > The env of of computer is:
> > CPLUS_INCLUDE_PATH=/home/r.yu/include/
> > HOSTNAME=euphoria.imb.uq.edu.au
> > PVM_RSH=/usr/bin/ssh
> > SHELL=/bin/bash
> > TERM=xterm
> > OBJC_INCLUDE_PATH=/home/r.yu/include/
> > HISTSIZE=1000
> > SSH_CLIENT=10.100.1.167 58323 22
> > SSH_TTY=/dev/pts/0
> > USER=r.yu
> > LD_LIBRARY_PATH=/home/r.yu/lib/
> >
> >
> LS_COLORS=no=00:fi=00:di=01;34:ln=01;36:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.gz=01;31:*.bz2=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.avi=01;35:*.fli=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.ogg=01;35:*.mp3=01;35:*.wav=01;35:
> > CPATH=/home/r.yu/include/
> > PVM_ROOT=/usr/share/pvm3
> >
> >
> PATH=/home/r.yu/bin:/home/r.yu/amber11/bin:/home/r.yu/amber10/bin:/home/r.yu/bin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/opt/pbs/bin:/opt/pbs/etc
> > MAIL=/var/spool/mail/r.yu
> > C_INCLUDE_PATH=/home/r.yu/include/
> > LD_RUN_PATH=/home/r.yu/lib/:
> > PWD=/home/r.yu/a7-imi-mutants-explicit/07_Comprehensive
> > INPUTRC=/etc/inputrc
> > LANG=en_US.UTF-8
> > PS1=\[\033[01;32m\]\u.\h\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]\$
> > SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass
> > HOME=/home/r.yu
> > SHLVL=2
> > LOGNAME=r.yu
> > CVS_RSH=ssh
> > SSH_CONNECTION=10.100.1.167 58323 130.102.116.37 22
> > MPI_HOME=/home/r.yu/
> > LESSOPEN=|/usr/bin/lesspipe.sh %s
> > AMBERHOME=/home/r.yu/amber11
> > G_BROKEN_FILENAMES=1
> > _=/bin/env
> > OLDPWD=/home/r.yu
> >
> > This may be not the problem of your script, but I cannot use it until I
> > solve the last problem. In fact I also asked help from others,
> > unfortunately, no people can help me.
> >
> > Best Regards,
> > Rilei Yu
> >
> > --- 10年6月1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6月1日,周二,上午8:29
> >
> > Excellent. I will figure out how we should add patches to the program on
> > the website, thanks for catching this one.
> >
> > As for the difference in the harmonic and quasi-harmonic approximations:
> I
> > don't know the specifics, but I believe the quasi-harmonic approximation
> > utilizes the covariance matrices (weighted by the mass of the particles)
> of
> > the systems and diagonalizes them to obtain the corresponding eigenvalues
> > and eigenvectors, wherein it treats the eigenvalues as vibrational
> > frequencies. Thus, it constructs a single matrix from all of the
> snapshots
> > (akin to PCA).
> >
> > Normal Mode analysis, on the other hand, constructs the hessian matrix
> for
> > each (minimized) snapshot and diagonalizes that, obtaining the
> vibrational
> > frequencies and computing the entropy based on that in a manner similar
> to
> > the quasi-harmonic approach. However, the normal mode analysis is
> > different
> > because only a single structure, theoretically located at a local minimum
> > on
> > the potential energy surface well-approximated by a harmonic potential,
> is
> > used to calculate the entropy. The QH approach takes snapshots from all
> > sorts of local minima to construct the matrix, leading it to be quite
> > frame-dependent (i.e. it depends on the number of frames you have), and
> it
> > can take a very large number of frames to converge (and you will get a
> much
> > much larger value than nmode calculations). QH is faster because you
> only
> > have to do one diagonalization, and I believe (though I'm not sure!) that
> > the covariance matrix is quite faster to compute than the hessian which
> is
> > used for normal mode analysis (another difference I forgot to mention
> > explicitly above).
> >
> > Hopefully this helped a little (I think the AmberTools manual has some
> > references under the "matrix" and "analyze matrix" keywords for ptraj).
> If
> > I made some fundamental errors in my explanation, someone please correct
> > me,
> > I have not studied these in depth.
> >
> > Good luck!
> > Jason
> >
> > On Mon, May 31, 2010 at 7:59 PM, Rilei Yu <yulaomao1983.yahoo.com.cn>
> > wrote:
> >
> > > Very thanks for both of you!
> > > After patched MMPBSA.py the problem is completely resolved!
> > > By the way, two approaches are used to calculate the entropy, one is
> > > ENTROPY RESULTS (QUASI-HARMONIC APPROXIMATION) CALCULATED WITH PTRAJ,
> and
> > > another is ENTROPY RESULTS (HARMONIC APPROXIMATION) CALCULATED WITH
> > NMODE.
> > > Can you briefly give me a brief introduction on the difference of them,
> > or
> > > you can recommend me some paper on that.
> > >
> > > Very appreciated for your help again!
> > >
> > > 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,下午9:07
> > >
> > > Hello Rilei,
> > >
> > > This is a bug. I'm not sure why it was even getting to that statement,
> > > since you were not attempting decomposition, anyway... I've attached a
> > > patch that should fix this problem.
> > >
> > > Put this file in the AMBERHOME directory in which you installed
> MMPBSA.py
> > > and type the following command:
> > >
> > > patch -p0 < mmpbsa.patch
> > >
> > > Also, the messages you were getting were not errors, like Bill said.
> > They
> > > indicate successful install of MMPBSA.py.
> > >
> > > After you apply this patch, it should work. Don't forget to "make
> > install"
> > > after you apply the patch, though, so the patched MMPBSA.py gets put in
> > the
> > > bin directory.
> > >
> > > Thanks!
> > > Jason
> > >
> > > 2010/5/31 Bill Miller III <brmilleriii.gmail.com>
> > >
> > > > Actually, it looks like everything is compiled correctly. You are
> > > properly
> > > > calling MMPBSA.py and ptraj from the Amber 11 directory, and sander
> > from
> > > > the
> > > > Amber 10 directory. It also appears you are correctly calling the new
> > > > version of Python since you did not get the same 'format' error as
> > > before.
> > > > Once again, there was not an error when you compiled MMPBSA.py. The
> > > > information printed is simply some helpful information and a
> > description
> > > of
> > > > the command the 'make install' is performing.
> > > >
> > > > Did you remove all the old MMPBSA.py files before running that
> command?
> > > You
> > > > should always do a 'MMPBSA.py --clean' before running a calculation
> to
> > > > remove all the old files. Or, you can add the '-O' flag to the
> command
> > > line
> > > > to overwrite all the old MMPBSA.py files that were made from a
> previous
> > > > calculation.
> > > >
> > > > -Bill
> > > >
> > > > On Mon, May 31, 2010 at 1:25 AM, Rilei Yu <yulaomao1983.yahoo.com.cn
> >
> > > > wrote:
> > > >
> > > > > Dear Dr. Jason,
> > > > >
> > > > > Based on your suggestion, I installed python 2.6.
> > > > >
> > > > > r.yu.euphoria:~/a7-imi-mutants-explicit/3000/a9s$ python -V
> > > > > Python 2.6.5
> > > > > I have uninstalled mmpbsa in amber10,
> > > > > then I recompiled mmpbsa in amber11. But there was error the same
> as
> > > > > former.
> > > > >
> > > > > 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
> > > > >
> > > > > I tried to run mmpbsa on a fomer file:
> > > > >
> > > > > &general
> > > > > startframe=1, endframe=1, interval=1, verbose=0,
> > > > > ligand_mask=':421-432', receptor_mask=':1-210:211-420',
> > > > > strip_mdcrd=1, #i also tried 0.
> > > > > /
> > > > > &gb
> > > > > saltcon=0.15, igb=5,
> > > > > /
> > > > > &pb
> > > > > istrng=0.15
> > > > > /
> > > > > r.yu.euphoria:~/a7-imi-mutants-explicit/3000/a9s$ MMPBSA.py -i
> > > > mmpbsa.in-sp complex_solvated.prmtop -cp complex.prmtop -rp re.prmtop
> > -lp
> > > > lig.prmtop
> > > > > -y complex_md0.mdcrd
> > > > > ptraj found! Using /home/r.yu/amber11/bin/ptraj
> > > > > sander found! Using /home/r.yu/amber10/bin/sander
> > > > > Assuming /home/r.yu/amber10/bin/sander is part of
> > > > > amber9 or amber10. Using old PB input file.
> > > > > Traceback (most recent call last):
> > > > > File "/home/r.yu/amber11/bin/MMPBSA.py", line 732, in <module>
> > > > > print >> 'Error: Energy decomposition only works with Amber11
> or
> > > > later
> > > > > for MMPBSA.py!'
> > > > >
> > > > > Is this to say, I failed to install python2.6 or anything else?
> > > > >
> > > > > Thanks for your response again!
> > > > >
> > > > > 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11:33
> > > > >
> > > > > Hello,
> > > > >
> > > > > We did not make the script more complicated, what we did was to
> > > introduce
> > > > > the .format syntax to improve the readability of the code. I was
> > > unaware
> > > > > that it didn't work for python 2.4 and earlier until the changes
> were
> > > > made.
> > > > > I found this out on one of our compute clusters that only had
> python
> > > 2.4
> > > > > installed.
> > > > >
> > > > > However, I got around this by installing python locally, which is
> > > > something
> > > > > you can do as well, you just have to install python locally. If you
> > can
> > > > find
> > > > > someone with sufficient unix knowledge to do this for you, it
> should
> > be
> > > > > easier. I'll include some quick instructions here that should work
> if
> > > you
> > > > > want to try it yourself.
> > > > >
> > > > > First download the python package and extract it into one of your
> > > > > directories. Go to the directory and execute the following
> commands:
> > > > >
> > > > > ./configure --prefix=$HOME
> > > > > make && make install
> > > > >
> > > > > This will build python in your home directory. Then set that
> > directory
> > > in
> > > > > your path first. So put in your .bashrc
> > > > >
> > > > > export PATH=~/bin\:$PATH
> > > > >
> > > > > This will make the correct python run mmpbsa.py. As for getting
> the
> > > old
> > > > > version of the script to work, I don't know why it's not working
> for
> > > your
> > > > > system and I don't really know what to try first because I don't
> have
> > > > your
> > > > > files and don't specifically know the problem. Hopefully the other
> > > > > instructions to get python 2.6 installed will work and you'll have
> > luck
> > > > with
> > > > > the new version. Also note that if you install mpi4py, you can run
> > the
> > > > nmode
> > > > > calculations in parallel, which should speed things up.
> > > > >
> > > > > Good luck!
> > > > > Jason
> > > > >
> > > > > --
> > > > > 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/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
> > > >
> > >
> > >
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Graduate Student
> > > 352-392-4032
> > >
> > > -----下面为附件内容-----
> > >
> > > _______________________________________________
> > > 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
> >
>
>
>
> --
> T. Dwight McGee Jr.
> Quantum Theory Project
> University of Florida
> dwight.mcgee.gmail.com
>
> "Problems cannot be solved at the same level of awareness that created
> them."
> Albert Einstein
> _______________________________________________
> 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 Wed Jun 02 2010 - 05:00:03 PDT
