Hello Jason,
Thank you for your help and suggestions.
As par your suggestions, I have downloaded the python2.7 and installed in my
computer.
Also have tested with the make test command. It all goes passed.
However when I am going to compile MMPBSA.py with the make serial command,
again it is showing the message like follows:
[root.compute-02-07 mmpbsa_py]# make serial
/bin/bash setup.sh
Python version 2 detected. No file conversion necessary.
/bin/cp MMPBSA.py *pyc /usr/apps/amber10/amber11/bin
/usr/apps/amber10/amber11/bin/nab -o mmpbsa_py_nabnmode mmpbsa_entropy.nab
/bin/mv mmpbsa_py_nabnmode /usr/apps/amber10/amber11/bin
Here, it is Python 2 is detected (although I have installed Python2.7). Is
there any tricky here ? How the system will detect Python2.7 ? Should I add
any path for the Python? Please let me know.
Thanks and best wishes
Siddharth
On Thu, Sep 16, 2010 at 7:49 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Hi Siddhath,
>
> This is actually a problem with your Python version. I used the
> ".format()"
> function in parts of MMPBSA.py not knowing that it was a feature introduced
> in Python 2.6 (Well, actually Python 3.0 and backported to Python 2.6).
> Therefore, the version of the source code that is available on the website
> will only work with Python 2.6 or later. I've gone back and rewritten the
> relevant parts of the code to make it backwards compatible with older
> versions of Python, but I haven't posted those files online yet. Hopefully
> I'll post the new source code online soon, since it'll relieve a lot of the
> installation headaches that people have been having with it.
>
> To get it to work now, you'll have to install a copy of Python2.6 or
> Python2.7 (Python3 and greater is not well tested, but it may work)
>
> Hope this helps!
> Jason
>
> On Thu, Sep 16, 2010 at 7:01 PM, Siddharth Rastogi <
> siddharthrastogi08.gmail.com> wrote:
>
> > Hello Jason,
> >
> > I have installed the serial version of MMPBSA.py in my computer and also
> > have applied all the patches.
> > When I was just following to calculate the binding free energy of the
> > Estrogen Receptor and Raloxifene using the files there in the
> > tutorial(whatever that is in the AMBER Tutorial Section 3.2), I got the
> > following errors.
> >
> > Traceback (most recent call last):
> > File "/usr/apps/amber10/amber11/bin/MMPBSA.py", line 629, in ?
> > utils.gbmdin(INPUT) # create our own
> > File "/usr/apps/amber10/amber11/src/mmpbsa_py/utils.py", line 329, in
> > gbmdin
> > mdin.write(
> > AttributeError: 'str' object has no attribute 'format'
> >
> > I just browsed the error in the archive and found some information in the
> > listing (http://archive.ambermd.org/201005/0950.html). According to your
> > reply to this question again I applied the patch file as follows:
> >
> > > patch -p0 < mmpbsa.patch
> >
> > However, the error returns like this:
> >
> > patching file src/mmpbsa_py/MMPBSA.py
> > Reversed (or previously applied) patch detected! Assume -R? [n] Yes
> > Apply anyway? [n] Yes
> > Skipping patch.
> > 1 out of 1 hunk ignored -- saving rejects to file
> > src/mmpbsa_py/MMPBSA.py.rejpatch: **** Can't remove file
> > src/mmpbsa_py/MMPBSA.py.rej : Permission denied
> >
> > >From here, I understood there may not be a patch problem, because
> > previously
> > I have applied all patches during installation. also again I performed
> the
> > "make install" command too. Then I typed as the command
> >
> > > /usr/apps/amber10/amber11/bin/MMPBSA.py -O -i mmpbsa_2b.in -o
> > FINAL_RESULTS_MMPBSAPY.dat -sp 1err.solvated.prmtop -cp complex.prmtop
> -rp
> > receptor.prmtop -lp ligand.prmtop -y *.mdcrd
> >
> > Even then NO luck.
> >
> > So can you please suggest me what may be the problem here.
> >
> > Thank you for your suggestions in advance.
> >
> > best wishes
> > Siddhath
> >
> > On Tue, Sep 14, 2010 at 12:49 PM, Jason Swails <jason.swails.gmail.com
> > >wrote:
> >
> > > Hello,
> > >
> > > There are two versions: MMPBSA.py.MPI and MMPBSA.py. MMPBSA.py is a
> > > single-processor version, whereas MMPBSA.py.MPI is the parallel
> processor
> > > version. In order to run MMPBSA.py.MPI, you must first install mpi4py,
> > and
> > > then you may use MMPBSA.py.MPI just as you would use MMPBSA.py. If you
> > > don't need MMPBSA.py.MPI, then you can just use MMPBSA.py without
> further
> > > adjustments.
> > >
> > > Instructions for use and installation can be found on the same tutorial
> > > website: http://ambermd.org/tutorials/advanced/tutorial3/py_script
> > >
> > > Good luck!
> > > Jason
> > >
> > > On Tue, Sep 14, 2010 at 12:29 PM, Siddharth Rastogi <
> > > siddharthrastogi08.gmail.com> wrote:
> > >
> > > > Dear Jason Swails,
> > > >
> > > > Thank you for your reply.
> > > > Initially I was doing the calculation with the mm_pbsa.pl version.
> > > > I don't know, how it worked with the tutorial and not for my case of
> > > > protein-ligand.
> > > >
> > > > Now, according to your suggestion, I am trying for the Python
> version.
> > > > But as I can see, this is the MPI version need to be installed.
> > > > However, I am doing my calculation in my single processor PC, with
> the
> > > > Amber10 installed in.
> > > > So, can you please let me know how to install the Python version and
> > what
> > > > will be the steps to be followed for the installation of mpi4py and
> the
> > > > usage of MM-PBSA.MPI.py.
> > > >
> > > > Thanks in advance for your suggestions.
> > > >
> > > > Siddharth
> > > >
> > > >
> > > > On Wed, Sep 8, 2010 at 11:11 PM, Jason Swails <
> jason.swails.gmail.com
> > > > >wrote:
> > > >
> > > > > Hello,
> > > > >
> > > > > Have you considered trying the Python version? The source code and
> > > > > instructions for installation/use are included on the same tutorial
> > > > you're
> > > > > using now (
> http://ambermd.org/tutorials/advanced/tutorial3/py_script
> > ).
> > > > If
> > > > > you choose to use that version, please remember to apply the
> patches
> > > also
> > > > > located on that site.
> > > > >
> > > > > Good luck!
> > > > > Jason
> > > > >
> > > > > On Wed, Sep 8, 2010 at 8:49 PM, Siddharth Rastogi <
> > > > > siddharthrastogi08.gmail.com> wrote:
> > > > >
> > > > > > Hello Bill Ross,
> > > > > >
> > > > > > Thank you for your response and the suggestions.
> > > > > >
> > > > > > However, if I am going to the AMBER tutorial-3 regarding the
> > MM-PBSA
> > > > > > calculation, I can see the use of gas phase topology (prmtop)
> files
> > > in
> > > > > the
> > > > > > extracts_coords.mmpbsa and binding_energy.mmpbsa files with the
> use
> > > of
> > > > > > "ras-raf_solvated.prmtop"
> > > > > > to generate the trajectory files.
> > > > > >
> > > > > > Also, I wonder how these works in the tutorial. I am a bit
> confused
> > > > with
> > > > > > this. If I am wrong, rectify me.
> > > > > >
> > > > > > Does your trajectory files (prod_1.mdcrd, prod_2.mdcrd...)
> contain
> > > > water
> > > > > > molecules ?
> > > > > >
> > > > > > I just wanted to calculate the binding free energy between the
> > > > > > protein-ligand complex of a solvated system. Please do suggest me
> > the
> > > > > right
> > > > > > path.
> > > > > >
> > > > > > Thanks
> > > > > > Siddharth
> > > > > >
> > > > > >
> > > > > > On Fri, Sep 3, 2010 at 8:14 PM, Bill Ross <ross.cgl.ucsf.edu>
> > wrote:
> > > > > >
> > > > > > > > FATAL: NATOM mismatch in coord and topology files.
> > > > > > >
> > > > > > > The prmtop for a solvated system cannot be used with crds for
> the
> > > > > vacuum
> > > > > > > version and vice-versa.
> > > > > > >
> > > > > > > Bill
> > > > > > >
> > > > > > > _______________________________________________
> > > > > > > AMBER mailing list
> > > > > > > AMBER.ambermd.org
> > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > Siddharth Rastogi
> > > > > > _______________________________________________
> > > > > > 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
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Siddharth Rastogi
> > > > _______________________________________________
> > > > 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
> > >
> >
> >
> >
> > --
> > Siddharth Rastogi
> > _______________________________________________
> > 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
>
--
Siddharth Rastogi
_______________________________________________
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Received on Thu Sep 23 2010 - 15:30:08 PDT
