Re: [AMBER] MCPB problem

From: Pengfei Li <ambermailpengfei.gmail.com>
Date: Fri, 11 Sep 2015 11:56:14 -0400

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
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Received on Fri Sep 11 2015 - 09:00:05 PDT
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