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
Received on Mon May 31 2010 - 17:00:07 PDT
