Hi Kshatresh,
It seems the error implies that you did not install scipy in the machine.
Can you do a quick check by using the following command *python -c "import
scipy"*, if there is error raised, which means you did not install scipy
indeed.
Best,
Pengfei
2015-09-12 10:45 GMT-04:00 Kshatresh Dutta Dubey <kshatresh.gmail.com>:
> HI Pengfei,
>
> I am facing a new problem during MCPB.py run after installing AmberTool 15.
> It seems to me something is wrong with python interpreter, but other
> programs like MMPBSA.py is running fine with same installations. I have
> correctly defined the python environment as it is mentioned in amber.sh. I
> am getting following error during MCPB.py :
>
> Traceback (most recent call last):
> File "/usr/local/amber14/bin/MCPB.py", line 46, in <module>
> from mcpb.gene_model_files import get_ms_resnames, gene_model_files
> File
> "/usr/local/amber14/lib/python2.7/site-packages/mcpb/gene_model_files.py",
> line 13, in <module>
> from pymsmtlib.lib import get_lib_dict
> File "/usr/local/amber14/lib/python2.7/site-packages/pymsmtlib/lib.py",
> line 8, in <module>
> from scipy.optimize import curve_fit
> ImportError: No module named scipy.optimize
>
> Please help me to figure out the problem.
>
> Thanking you
> Kshatresh
>
>
> On Fri, Sep 11, 2015 at 7:19 PM, Pengfei Li <ambermailpengfei.gmail.com>
> wrote:
>
> > Hi Kshatresh,
> >
> > It also supports Zn. The following words in the tutorial may be
> confusing:
> >
> > Z-matrix methodThe bond and angle force constants are determined from the
> > Cartesian Hessian matrixSeminario MethodThe bond and angle force
> constants
> > are determined from the sub matrices of the Cartesian Hessian
> > matrixEmpirical
> > Method (Only in MCPB.py)The bond and angle force constants are determined
> > from an empirical method developed by Li et al. in Merz Research Group,
> > current version only supports bonded model of Zinc ion
> >
> > Actually it means, MCPB supports two methods (Z-matrix and Seminario),
> > while MCPB.py supports three methods (Z-matrix, Seminario and an
> empirical
> > one). The empirical method in MCPB.py only supports Zn ion now but for
> the
> > other two methods in MCPB.py they support a lot of ions.
> >
> > Best,
> > Pengfei
> >
> > 2015-09-11 12:15 GMT-04:00 Kshatresh Dutta Dubey <kshatresh.gmail.com>:
> >
> > > Hi Pengfei
> > >
> > > Thanks for your reply. Does the python version also support for Fe?
> Some
> > > time ago I read that present version supports only for Zn.
> > >
> > > On Fri, Sep 11, 2015 at 6:56 PM, Pengfei Li <
> ambermailpengfei.gmail.com>
> > > wrote:
> > >
> > > > Dear Kshatresh,
> > > >
> > > > There is a program called MCPB.py, a python substitute of MCPB, in
> > > > AmberTools15 (AmberTools15 is free and you can download it here:
> > > > http://ambermd.org/AmberTools15-get.html). It takes much less time
> to
> > > > parameterize a metal site by using MCPB.py than MCPB. There is also a
> > web
> > > > tutorial about MCPB.py:
> > > > http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm. If you
> > have
> > > > more questions, please feel free to email me.
> > > >
> > > > Best,
> > > > Pengfei
> > > >
> > > >
> > > > 2015-09-10 16:25 GMT-04:00 Kshatresh Dutta Dubey <
> kshatresh.gmail.com
> > >:
> > > >
> > > > > Dear Users,
> > > > >
> > > > > I am using MCPB for building parameter of iron containing protein.
> I
> > am
> > > > > following exactly the same steps as described in MCPB tutorial,
> > > however I
> > > > > am getting problem in copying StdResidue in during _sidechain.bcl,
> > > > > particularly to the line describing metal (FE). I am attaching my
> > > > > _sidechain.bcl as well as pdb file.
> > > > > Please help me to fix this problem
> > > > >
> > > > > --
> > > > > With best regards
> > > > >
> > > > >
> > > >
> > >
> >
> ************************************************************************************************
> > > > > Kshatresh Dutta Dubey
> > > > > Post Doctoral Researcher,
> > > > > Lise Meitner Center for Computational Quantum Chemistry
> > > > > Hebrew University of Jerusalem Israel
> > > > > Jerusalem, Israel
> > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > > >
> > > >
> > > >
> > > > --
> > > > Pengfei Li
> > > > Ph.D. Candidate
> > > > Merz Research Group
> > > > Department of Chemistry
> > > > Michigan State University
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > With best regards
> > >
> > >
> >
> ************************************************************************************************
> > > Kshatresh Dutta Dubey
> > > Post Doctoral Researcher,
> > > Lise Meitner Center for Computational Quantum Chemistry
> > > Hebrew University of Jerusalem Israel
> > > Jerusalem, Israel
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Pengfei Li
> > Ph.D. Candidate
> > Merz Research Group
> > Department of Chemistry
> > Michigan State University
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> With best regards
>
> ************************************************************************************************
> Kshatresh Dutta Dubey
> Post Doctoral Researcher,
> Lise Meitner Center for Computational Quantum Chemistry
> Hebrew University of Jerusalem Israel
> Jerusalem, Israel
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Pengfei Li
Ph.D. Candidate
Merz Research Group
Department of Chemistry
Michigan State University
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Received on Sat Sep 12 2015 - 17:00:03 PDT
