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
Received on Thu Sep 16 2010 - 17:00:05 PDT
