Dear amber users very thanks your help again,
Based on your suggestion, I do such change as:
/home/r.yu/Python-2.6.5/python /home/ryu/amber11/bin/MMPBSA.py
Now, I believe it should can work.
Rilei Yu
--- 10年6月2日，周三, 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2日,周三,下午9:14
Hello,
Do not define your PATH inside your submission script. What is happening is
the compute node is having PATH redefined, so it's getting the system python
first (python version 2.4), whereas you used python version 2.6 to compile
the python modules.
Take out the definition of PATH (setenv PATH), and just allow your .bashrc
to define the path properly.
You should probably also use the bash shell if that's what you use
interactively. Change the top line from #!/bin/csh to #!/bin/bash to do
this (and change all csh syntax to bash syntax). This will make sure the
new session sources your .bashrc, rather than a non-existent .cshrc. Of
course, if your interactive shell is csh, then keep csh.
If you are still having trouble with this, you can manually specify the
correct python to use on the command-line with MMPBSA.py:
/home/r.yu/bin/python MMPBSA.py -O -i ...
PYTHONPATH only provides python with places to look for imported python
modules.
Good luck!
Jason
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
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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 Wed Jun 02 2010 - 18:00:03 PDT
