OK, thanks for all the help. I got it to work using your advice plus a
slight modification.
For anyone's reference, here is my workflow:
(symbolic link x86_64-apple.. compilers to make sure they are first in the
path)
then after downloading the bugfixes, netcdf-4.1.3 and openmpi-1.4.3,
tar -xvjf source/AmberTools-1.5*
tar -xvjf source/Amber11.tar.bz2
cd amber11
patch -p0 -N < ../amberstuff/A.bugfix.all
cd Ambertools/src
mv netcdf oldnetcdf
mkdir netcdf
cd netcdf
tar -xvzf /Users/sindhikara/MyPrograms/source/netcdf-4.1.3.tar.gz
mv netcdf-4.1.3 src
cd ..
./configure -macAccelerate -nopython gnu > dan.out.1
make install > dan.out.2
cd ../../
patch -p0 -N < ../amberstuff/bugfix.all
./AT15_Amber11.py
cd src
make serial > dan.out.3
cd ../Ambertools/src
tar -xvjf ../../../source/openmpi-1.4.3.tar.bz2
./configure_openmpi -np 8 gnu > dan.out.4
rehash
make clean
./configure -macAccelerate -mpi gnu > dan.out.5
make install > dan.out.6
cd ../../
./AT15_Amber11.py
cd src
make clean
make parallel > dan.out.7
20-111/7/27 Takeshi Baba <tbaba.cheng.es.osaka-u.ac.jp>
> Dear Sindhikara
>
> Hi
>
> In my case, I didn't change the configure.
> I made the link gcc >x86_64-aple-drawin10-gcc-4.5.3
> g++>x86_64-aple-drawin10-g++-mp-4.5
> gfortran>x86_64-aple-drawin10-gfortran-
> mp-4.5
>
> If you did the following method
> >>>>>>>> cp ~/netcdf-4.1.3.tar .
> >>>>>>>> mv netcdf netcdf_old
> >>>>>>>> mkdir netcdf
> >>>>>>>> cd netcdf
> >>>>>>>> tar -xvf ../netcdf-4.1.3.tar
> >>>>>>>> mv netcdf-4.1.3/ src
> ,you don't have to change the configure.
>
> If you have the problem in the netcdf,plase make configure in your
> netcdf directory.
>
>
> Good luck......
>
> Takeshi
>
> On 2011/07/26, at 18:41, Daniel Sindhikara wrote:
>
> > Jason,
> > Thanks, yes that did fix *that* problem (despite it not making
> > sense).
> >
> > Takeshi, you gave instructions on each step but have a modified
> > version of
> > configure and a separate netcdf. What is different about the
> > configure and
> > netcdf? About 'linking gcc45', did you only link gcc45 or also
> > gfortran and
> > g++?
> >
> > --Dan
> >
> > On Tue, Jul 26, 2011 at 10:32 AM, Jason Swails
> > <jason.swails.gmail.com>wrote:
> >
> >> Try configuring with -nopython. It should still be able to run the
> >> Python
> >> programs there.
> >>
> >> However, I haven't had issues building Python on my Mac. It should
> >> use the
> >> Xcode GCC by default. I haven't followed the thread long enough,
> >> but I can
> >> look into it more in a week or so.
> >>
> >> HTH,
> >> Jason
> >>
> >> --
> >> Jason M. Swails
> >> Quantum Theory Project,
> >> University of Florida
> >> Ph.D. Candidate
> >> 352-392-4032
> >>
> >> On Jul 25, 2011, at 3:10 AM, Daniel Sindhikara <sindhikara.gmail.com>
> >> wrote:
> >>
> >>> Takeshi,
> >>> It took a while to reply, sorry about that. I understand that it
> >>> worked
> >>> for you but I'm still getting the same permissions error when I
> >>> try to
> >>> install. I am using gcc 4.5 from macports, but I still don't see
> >>> how that
> >> is
> >>> related to the python permissions error. In your workflow I don't
> >>> see
> >>> anything about python. Are you saying I should replace the python
> >>> 2.6.6
> >>> directory with 2.6?
> >>> -Dan
> >>>
> >>> 2011/7/14 Takeshi Baba <tbaba.cheng.es.osaka-u.ac.jp>
> >>>
> >>>> Now I tried to install amber11 on the Mac OS10.6.8
> >>>>
> >>>>
> >>>> Before installing amber11, I got gcc45 from Macports and make a
> >>>> link
> >>>>
> >>>>>>>> My method to install amber11
> >>>>>>>> ===============================
> >>>>>>>> patch -p0 -N < bugfix.all.A.txt (AmberTool bug fix)
> >>>>>>>> cd AmberTools/src
> >>>>>>>> cp ~/netcdf-4.1.3.tar .
> >>>>>>>> mv netcdf netcdf_old
> >>>>>>>> mkdir netcdf
> >>>>>>>> cd netcdf
> >>>>>>>> tar -xvf ../netcdf-4.1.3.tar
> >>>>>>>> mv netcdf-4.1.3/ src
> >>>>>>>> cd ../
> >>>>>>>> ./configure.tbaba -macAccelerate gnu
> >>>>>>>> make install
> >>>>>>>> cd ../../
> >>>>>>>> patch -p0 -N < ../bugfix.all_11.txt
> >>>>>>>> ./AT15_Amber11.py
> >>>>>>>> cd src
> >>>>>>>> make serial
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> ===============================
> >>>>>>
> >>>>
> >>>>
> >>>> I succeeded in installing amber11 (serial)
> >>>>
> >>>> *My machine is iMac .
> >>>>
> >>>> If you have a time you should start from the following command.
> >>>>
> >>>> tar xvfj AmberToos-1.5.tar.bz2
> >>>>
> >>>>
> >>>> Good luck
> >>>>
> >>>> Takeshi Baba
> >>>>
> >>>> On 2011/07/14, at 11:44, Daniel Sindhikara wrote:
> >>>>
> >>>>> I'm not sure what you mean here. Python 2.6.6 is included in the
> >>>>> ambertools
> >>>>> tarball.
> >>>>> Are you saying I should replace it with a different version?
> >>>>>
> >>>>>
> >>>>> 2011/7/13 Takeshi Baba <tbaba.cheng.es.osaka-u.ac.jp>
> >>>>>
> >>>>>> Hi
> >>>>>> you check the python in your configure.
> >>>>>> I think you should use gcc4.2 to install Python2.6 in the
> >>>>>> amber11.
> >>>>>>
> >>>>>> when you make clean in the ambertools, Python2.6.6 is removed.
> >>>>>> So you try to start to unzip ambertools again.
> >>>>>>
> >>>>>> If you get something wrong or same problems,
> >>>>>> please give me a mail
> >>>>>>
> >>>>>> good luck.
> >>>>>>
> >>>>>> Takeshi Baba
> >>>>>> On 2011/07/13, at 20:01, Daniel Sindhikara wrote:
> >>>>>>
> >>>>>>> Thanks all for the help so far, but..
> >>>>>>> A few points:
> >>>>>>> 1) It is AT 1.5
> >>>>>>> 2) I did apply the bugfix.
> >>>>>>> 3) Under dac's warning, I reinstalled from scratch into a non
> >>>>>>> "root"
> >>>>>>> directory
> >>>>>>> 4) Now I have a new problem. If I unzip ambertools, patch, ./
> >>>>>>> configure
> >>>>>>> -macAccelerate gnu, then make install, I get a permissions
> >>>>>>> problem.
> >>>>>>> Part of
> >>>>>>> the python install wants to write to my /Applications/..
> >>>>>>> directory
> >>>>>>>
> >>>>>>> Considering I'm rebuilding from scratch (I completely removed my
> >>>>>>> previous
> >>>>>>> installation) I don't see where the problem is coming from
> >>>>>>> unless I
> >>>>>>> caused
> >>>>>>> some damage with my previous sudo usage.
> >>>>>>>
> >>>>>>> Appreciate any ideas...
> >>>>>>>
> >>>>>>> ...
> >>>>>>> /usr/bin/install -c -s ../python.exe
> >>>>>>> "/Users/sindhikara/MyPrograms/amber11/Python.framework/
> >>>>>>> Versions/2.6/
> >>>>>>> Resources/Python.app/Contents/MacOS/Python"
> >>>>>>> sed -e "s!%bundleid%!org.python.python!g" \
> >>>>>>> -e
> >>>>>>> "s!%version%!`DYLD_FRAMEWORK_PATH=/Users/sindhikara/MyPrograms/
> >>>>>>> amber11/AmberTools/src/etc/Python-2.6.6:
> >>>>>>> ../python.exe \
> >>>>>>> -c 'import platform; print(platform.python_version())'`!g" \
> >>>>>>> <
> >>>>>>> "/Users/sindhikara/MyPrograms/amber11/Python.framework/
> >>>>>>> Versions/2.6/
> >>>>>>> Resources/Python.app/Contents/
> >>>>>>> Info.plist.in" \
> >>>>>>>>
> >>>>>>> "/Users/sindhikara/MyPrograms/amber11/Python.framework/
> >>>>>>> Versions/2.6/
> >>>>>>> Resources/Python.app/Contents/Info.plist"
> >>>>>>> rm
> >>>>>>> "/Users/sindhikara/MyPrograms/amber11/Python.framework/
> >>>>>>> Versions/2.6/
> >>>>>>> Resources/Python.app/Contents/
> >>>>>>> Info.plist.in"
> >>>>>>> DYLD_FRAMEWORK_PATH=/Users/sindhikara/MyPrograms/amber11/
> >>>>>>> AmberTools/
> >>>>>>> src/etc/Python-2.6.6:
> >>>>>>> ../python.exe ./scripts/BuildApplet.py \
> >>>>>>> --destroot "" \
> >>>>>>>
> >>>>>>> --python=/Users/sindhikara/MyPrograms/amber11/Python.framework/
> >>>>>>> Versions/2.6/Resources/Python.app/Contents/MacOS/Python`test
> >>>>>>> -f
> >>>>>>> "/Users/sindhikara/MyPrograms/amber11/Python.framework/
> >>>>>>> Versions/2.6/
> >>>>>>> Resources/Python.app/Contents/MacOS/Python-32"
> >>>>>>> && echo "-32"` \
> >>>>>>> --output "/Applications/Python 2.6/Build Applet.app" \
> >>>>>>> ./scripts/BuildApplet.py
> >>>>>>> ./scripts/BuildApplet.py:37: DeprecationWarning: catching of
> >>>>>>> string
> >>>>>>> exceptions is deprecated
> >>>>>>> except buildtools.BuildError, detail:
> >>>>>>> Traceback (most recent call last):
> >>>>>>> File "./scripts/BuildApplet.py", line 159, in <module>
> >>>>>>> main()
> >>>>>>> File "./scripts/BuildApplet.py", line 36, in main
> >>>>>>> buildapplet()
> >>>>>>> File "./scripts/BuildApplet.py", line 126, in buildapplet
> >>>>>>> progress=verbose, destroot=destroot)
> >>>>>>> File
> >>>>>>> "/Users/sindhikara/MyPrograms/amber11/AmberTools/src/etc/
> >>>>>>> Python-2.6.6/Lib/plat-mac/buildtools.py",
> >>>>>>> line 122, in process
> >>>>>>> copy_codefragment, raw, others, filename, destroot)
> >>>>>>> File
> >>>>>>> "/Users/sindhikara/MyPrograms/amber11/AmberTools/src/etc/
> >>>>>>> Python-2.6.6/Lib/plat-mac/buildtools.py",
> >>>>>>> line 151, in process_common
> >>>>>>> is_update, raw, others, filename, destroot)
> >>>>>>> File
> >>>>>>> "/Users/sindhikara/MyPrograms/amber11/AmberTools/src/etc/
> >>>>>>> Python-2.6.6/Lib/plat-mac/buildtools.py",
> >>>>>>> line 338, in process_common_macho
> >>>>>>> builder.build()
> >>>>>>> File
> >>>>>>> "/Users/sindhikara/MyPrograms/amber11/AmberTools/src/etc/
> >>>>>>> Python-2.6.6/Lib/plat-mac/bundlebuilder.py",
> >>>>>>> line 150, in build
> >>>>>>> shutil.rmtree(self.bundlepath)
> >>>>>>> File
> >>>>>>> "/Users/sindhikara/MyPrograms/amber11/AmberTools/src/etc/
> >>>>>>> Python-2.6.6/Lib/shutil.py",
> >>>>>>> line 212, in rmtree
> >>>>>>> rmtree(fullname, ignore_errors, onerror)
> >>>>>>> File
> >>>>>>> "/Users/sindhikara/MyPrograms/amber11/AmberTools/src/etc/
> >>>>>>> Python-2.6.6/Lib/shutil.py",
> >>>>>>> line 217, in rmtree
> >>>>>>> onerror(os.remove, fullname, sys.exc_info())
> >>>>>>> File
> >>>>>>> "/Users/sindhikara/MyPrograms/amber11/AmberTools/src/etc/
> >>>>>>> Python-2.6.6/Lib/shutil.py",
> >>>>>>> line 215, in rmtree
> >>>>>>> os.remove(fullname)
> >>>>>>> OSError: [Errno 13] Permission denied: '/Applications/Python
> >>>>>>> 2.6/
> >>>>>>> Build
> >>>>>>> Applet.app/Contents/Info.plist'
> >>>>>>> make[2]: *** [install_BuildApplet] Error 1
> >>>>>>> make[1]: *** [frameworkinstallapps] Error 2
> >>>>>>> make: *** [python] Error 2
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> 2011/7/12 Takeshi Baba <tbaba.cheng.es.osaka-u.ac.jp>
> >>>>>>>
> >>>>>>>> Dear Dr. Daniel J. Sindhikara
> >>>>>>>>
> >>>>>>>> Hi
> >>>>>>>> I succeed in installing amber11 & AmberTools1.5 on the Mac a
> >>>>>>>> few
> >>>>>>>> days
> >>>>>>>> ago.
> >>>>>>>>
> >>>>>>>> When I installed amber11, I got the same problems.
> >>>>>>>>
> >>>>>>>> So In my case I changed the netcdf to the latest
> >>>>>>>> $B!J(B4.1.3) .
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> My method may not useful for your install.
> >>>>>>>> Because my Mac is 10.5.8.
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> My method to install amber11
> >>>>>>>> ===============================
> >>>>>>>> patch -p0 -N < bugfix.all.A.txt (AmberTool bug fix)
> >>>>>>>> cd AmberTools/src
> >>>>>>>> cp ~/netcdf-4.1.3.tar .
> >>>>>>>> mv netcdf netcdf_old
> >>>>>>>> mkdir netcdf
> >>>>>>>> cd netcdf
> >>>>>>>> tar -xvf ../netcdf-4.1.3.tar
> >>>>>>>> mv netcdf-4.1.3/ src
> >>>>>>>> cd ../
> >>>>>>>> ./configure.tbaba -macAccelerate gnu
> >>>>>>>> make install
> >>>>>>>> cd ../../
> >>>>>>>> patch -p0 -N < ../bugfix.all_11.txt
> >>>>>>>> ./AT15_Amber11.py
> >>>>>>>> cd src
> >>>>>>>> make serial
> >>>>>>>> cd ../AmberTools/src
> >>>>>>>> cp ~/openmpi-1.4.3.tar .
> >>>>>>>> tar -xvf openmpi-1.4.3.tar
> >>>>>>>> ./configure_openmpi -np 8 gnu
> >>>>>>>> rehash
> >>>>>>>> make clean
> >>>>>>>> ./configure.tbaba -macAccelerate -mpi gnu
> >>>>>>>>
> >>>>>>>> make install
> >>>>>>>> cd ../../
> >>>>>>>> ./AT15_Amber11.py
> >>>>>>>> cd src/
> >>>>>>>> make clean
> >>>>>>>> make parallel
> >>>>>>>> ===============================
> >>>>>>>>
> >>>>>>>> If you try my method, you should the following command
> >>>>>>>>
> >>>>>>>> tar xvfj Amber11.tar.bz2
> >>>>>>>>
> >>>>>>>> If you have a question, please give me a mail.
> >>>>>>>>
> >>>>>>>> Good luck
> >>>>>>>>
> >>>>>>>> Takeshi Baba
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>
> >>>>
> >>
> ----------------------------------------------------------------------------------------------------
> >>>>>>>> Takeshi Baba
> >>>>>>>>
> >>>>>>>> Graduate School of Life Science, University of Hyogo,
> >>>>>>>> 3-2-1 Koto, Kamigori, Akoh-gun, Hyogo 678-1297, Japan
> >>>>>>>> E-mail: tbaba.cheng.es.osaka-u.ac.jp
> >>>>>>>>
> >>>>>>>>
> >>>>>>
> >>>>
> >>
> ----------------------------------------------------------------------------------------------------
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> On 2011/07/12, at 20:35, Daniel Sindhikara wrote:
> >>>>>>>>
> >>>>>>>>> Hello.
> >>>>>>>>> I am trying to run AMBER11 on a mac. I have been using
> >>>>>>>>> Ambertools
> >>>>>>>>> successfully, but when I try to make serial in the
> >>>>>>>>> $AMBERHOME/src/
> >>>>>>>>> directory
> >>>>>>>>> I get some undefined symbols when trying to make sander (from
> >>>>>>>>> command sudo
> >>>>>>>>> make serial).
> >>>>>>>>> My system is running Mac OSX10.6.8. I configured using ./
> >>>>>>>>> configure
> >>>>>>>>> -macAccelerate gnu
> >>>>>>>>>
> >>>>>>>>> Anyone run into this issue?
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> Here is the start of the errors:
> >>>>>>>>> gfortran-mp-4.5 -o sander constants.o state.o memory_module.o
> >>>>>>>>> stack.o
> >>>>>>>>> nose_hoover.o nose_hoover_vars.o nose_hoover_init.o
> >>>>>>>>> qmmm_module.o
> >>>>>>>>> trace.o
> >>>>>>>>> lmod.o rand2.o lmodC.o xminC.o decomp.o icosasurf.o egb.o
> >>>>>>>>> remd.o
> >>>>>>>>> findmask.o
> >>>>>>>>> relax_mat.o nmr.o multitmd.o multisander.o sander.o trajene.o
> >>>>>>>>> cshf.o
> >>>>>>>>> nmrcal.o mtmdcall.o pearsn.o printe.o runmin.o rdparm.o
> >>>>>>>>> mdread.o
> >>>>>>>>> locmem.o
> >>>>>>>>> runmd.o getcor.o degcnt.o decnvh.o fastwt.o parallel.o shake.o
> >>>>>>>>> ene.o
> >>>>>>>>> mdwrit.o minrit.o set.o dynlib.o mdfil.o nmlsrc.o ew_force.o
> >>>>>>>>> ew_setup.o
> >>>>>>>>> ew_box.o ew_bspline.o ew_fft.o nonbond_list.o short_ene.o
> >>>>>>>>> ew_recip.o
> >>>>>>>>> pcshift.o align.o csa.o rfree.o rgroup.o amopen.o debug.o
> >>>>>>>>> ew_recip_reg.o
> >>>>>>>>> ew_handle_dips.o ew_dipole_recip.o mexit.o new_time.o
> >>>>>>>>> extra_pts.o
> >>>>>>>>> thermo_int.o matinv.o assert.o mmtsb.o mmtsb_client.o
> >>>>>>>>> erfcfun.o
> >>>>>>>>> constantph.o
> >>>>>>>>> prn_dipoles.o ips.o sglds.o iwrap2.o amoeba_valence.o
> >>>>>>>>> amoeba_multipoles.o
> >>>>>>>>> amoeba_recip.o amoeba_interface.o amoeba_direct.o
> >>>>>>>>> amoeba_mdin.o
> >>>>>>>>> amoeba_adjust.o amoeba_self.o amoeba_vdw.o amoeba_induced.o
> >>>>>>>>> amoeba_runmd.o
> >>>>>>>>> bintraj.o spatial_recip.o spatial_fft.o parms.o softcore.o
> >>>>>>>>> mbar.o
> >>>>>>>>> molecule.o
> >>>>>>>>> xref.o dssp.o charmm.o qm_mm.o qm_ewald.o
> >>>>>>>>> qm2_variable_solvent.o
> >>>>>>>>> qmmm_qmtheorymodule.o \
> >>>>>>>>> pimd_vars.o pimd_force.o pimd_init.o cmd_vars.o
> >>>>>>>>> cmd_matrix.o
> >>>>>>>>> lscivr_vars.o lsc_init.o lsc_xp.o force.o /usr/local/amber11/
> >>>>>>>>> lib/
> >>>>>>>>> libsqm.a \
> >>>>>>>>> mt19937.o ncsu-abmd-hooks.o ncsu-bbmd-ctxt.o ncsu-bbmd-
> >>>>>>>>> hooks.o
> >>>>>>>>> ncsu-cftree.o ncsu-colvar-math.o ncsu-colvar-type.o ncsu-
> >>>>>>>>> colvar-
> >>>>>>>>> utils.o
> >>>>>>>>> ncsu-colvar.o ncsu-constants.o ncsu-cv-ANGLE.o ncsu-cv-
> >>>>>>>>> DISTANCE.o
> >>>>>>>>> ncsu-cv-HANDEDNESS.o ncsu-cv-MULTI_RMSD.o ncsu-cv-N_OF_BONDS.o
> >>>>>>>>> ncsu-cv-N_OF_STRUCTURES.o ncsu-cv-R_OF_GYRATION.o ncsu-cv-
> >>>>>>>>> TORSION.o
> >>>>>>>>> ncsu-cv-LCOD.o ncsu-cv-COS_OF_DIHEDRAL.o ncsu-lexer.o ncsu-
> >>>>>>>>> parser.o
> >>>>>>>>> ncsu-pmd-hooks.o ncsu-rmsd.o ncsu-sander-hooks.o ncsu-sander-
> >>>>>>>>> proxy.o
> >>>>>>>>> ncsu-smd-hooks.o ncsu-umbrella.o ncsu-utils.o ncsu-value.o \
> >>>>>>>>> /usr/local/amber11/lib/libFpbsa.a /usr/local/amber11/lib/
> >>>>>>>>> arpack.a
> >>>>>>>>> -framework Accelerate ../../AmberTools/src/lib/nxtsec.o \
> >>>>>>>>> ../../AmberTools/src/lib/sys.a /usr/local/amber11/lib/
> >>>>>>>>> libnetcdf.a
> >>>>>>>>> Undefined symbols:
> >>>>>>>>> "_nf_put_varm_real_", referenced from:
> >>>>>>>>> ___netcdf_MOD_nf90_put_var_7d_fourbytereal in
> >>>>>>>>> libnetcdf.a(netcdf.o)
> >>>>>>>>> ___netcdf_MOD_nf90_put_var_6d_fourbytereal in
> >>>>>>>>> libnetcdf.a(netcdf.o)
> >>>>>>>>> ___netcdf_MOD_nf90_put_var_5d_fourbytereal in
> >>>>>>>>> libnetcdf.a(netcdf.o)
> >>>>>>>>> ___netcdf_MOD_nf90_put_var_4d_fourbytereal in
> >>>>>>>>> libnetcdf.a(netcdf.o)
> >>>>>>>>> ___netcdf_MOD_nf90_put_var_3d_fourbytereal in
> >>>>>>>>> libnetcdf.a(netcdf.o)
> >>>>>>>>> ___netcdf_MOD_nf90_put_var_2d_fourbytereal in
> >>>>>>>>> libnetcdf.a(netcdf.o)
> >>>>>>>>> ___netcdf_MOD_nf90_put_var_1d_fourbytereal in
> >>>>>>>>> libnetcdf.a(netcdf.o)
> >>>>>>>>> "_nf_delete_", referenced from:
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> --
> >>>>>>>>> Dr. Daniel J. Sindhikara
> >>>>>>>>> Institute for Molecular Science
> >>>>>>>>> E-mail: sindhikara.gmail.com
> >>>>>>>>> Website: http://sites.google.com/site/dansindhikara/
> >>>>>>>>> --
> >>>>>>>>> _______________________________________________
> >>>>>>>>> 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
> >>>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> --
> >>>>>>> Dr. Daniel J. Sindhikara
> >>>>>>> Institute for Molecular Science
> >>>>>>> E-mail: sindhikara.gmail.com
> >>>>>>> Website: http://sites.google.com/site/dansindhikara/
> >>>>>>> --
> >>>>>>> _______________________________________________
> >>>>>>> AMBER mailing list
> >>>>>>> AMBER.ambermd.org
> >>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>
> >>
> ----------------------------------------------------------------------------------------------------
> >>>>>> Takeshi Baba
> >>>>>>
> >>>>>> Graduate School of Life Science, University of Hyogo,
> >>>>>> 3-2-1 Koto, Kamigori, Akoh-gun, Hyogo 678-1297, Japan
> >>>>>> E-mail: tbaba.cheng.es.osaka-u.ac.jp
> >>>>>>
> >>>>>>
> >>>>
> >>
> ----------------------------------------------------------------------------------------------------
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> AMBER mailing list
> >>>>>> AMBER.ambermd.org
> >>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> --
> >>>>> Dr. Daniel J. Sindhikara
> >>>>> Institute for Molecular Science
> >>>>> E-mail: sindhikara.gmail.com
> >>>>> Website: http://sites.google.com/site/dansindhikara/
> >>>>> --
> >>>>> _______________________________________________
> >>>>> AMBER mailing list
> >>>>> AMBER.ambermd.org
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>
> >>>>
> >>>>
> >>>>
> >>
> ----------------------------------------------------------------------------------------------------
> >>>> Takeshi Baba
> >>>>
> >>>> Graduate School of Life Science, University of Hyogo,
> >>>> 3-2-1 Koto, Kamigori, Akoh-gun, Hyogo 678-1297, Japan
> >>>> E-mail: tbaba.cheng.es.osaka-u.ac.jp
> >>>>
> >>>>
> >>
> ----------------------------------------------------------------------------------------------------
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>
> >>>
> >>>
> >>> --
> >>> Dr. Daniel J. Sindhikara
> >>> Institute for Molecular Science
> >>> E-mail: sindhikara.gmail.com
> >>> Website: http://sites.google.com/site/dansindhikara/
> >>> --
> >>> _______________________________________________
> >>> 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
> >>
> >
> >
> >
> > --
> > Dr. Daniel J. Sindhikara
> > Institute for Molecular Science
> > E-mail: sindhikara.gmail.com
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> --------------------------------------------------------------------------------------------------------
> $BGO>l(B $B9d;K(B $B!J(BTakeshi Baba)
> $BBg:eBg3XBg3X1!4pAC9)3X8&5f2JJ*<AAO...l962=3X9)3XNN0h(B
> E-mail: tbaba.cheng.es.osaka-u.ac.jp
> $B")(B560-8531
> $BBg:eI\K-Cf;TBT7s;3D.(B1-3
> $BBg:eBg3XBg3X1!4pAC9)3X8&5f2J(B $BJ*<AAO...l96(B $B2=3X9)3XNN0h(B
> $BCfLn8&5f<<(B
>
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--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
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Received on Sun Jul 31 2011 - 23:00:04 PDT
