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
>
> _______________________________________________
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> 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 - 09:00:05 PDT
