Hi,
Thanks for help. I found that python-scipy was not installed. I installed
scipy but still I am facing some problem and now the error is :
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
ImportError: No module named mcpb.gene_model_files
Please help me the to fix this issue.
On Sun, Sep 13, 2015 at 2:30 AM, Pengfei Li <ambermailpengfei.gmail.com>
wrote:
> 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
> _______________________________________________
> 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
_______________________________________________
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Received on Sat Sep 12 2015 - 19:30:07 PDT
