RE: AMBER: QM/MM in reaction pathways?

From: Ross Walker <>
Date: Tue, 28 Aug 2007 08:21:40 -0700

Hi Qiang,

Do you really expect to find a tutorial along the lines of "How to write a
PhD thesis about XXXXX?"

> I am calculating free energy of reaction of
> protein. I need some
> tutorial or document about this field.I have study tutorial
> "A Coupled
> Potential QM/MM Simulation". but I don't think it suit to me.
> Could somebody
> tell me some tutorial or document about this?

I suggest you go read the literature, read some text books, try out the
classical thermodynamic integration tutorial on the Amber website and then
try and do it with QM/MM.

Note you are probably the first person to ever try this with Amber 9. It
should work although I've never tested it. So be prepared to do some real
research and probably get yours hands dirty with some coding. Then perhaps
you will actually learn how to do something for yourself rather than
expecting to be spoon fed.

Good luck.

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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Received on Wed Aug 29 2007 - 06:07:38 PDT
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