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
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Received on Fri Sep 11 2015 - 09:30:06 PDT
