Hi Pengfei,
Thanks a lot for clearing the confusion.
Best regards
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
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Received on Fri Sep 11 2015 - 10:00:03 PDT
