Dear Dr. Markus
Thanks for your reply.
I have already used QM(AM1)/MM-MD for my simulation.
Now I want to calculate the binding energy using QM/MM energies. GB/PBSA scripts calculate MM energies only, in other words, all the system is treated by MM level.
So, how can I calculate the binding energies using QM/MM energies?
thanks for your help
Eliac
--- On Sun, 12/26/10, Markus Kaukonen <markus.kaukonen.iki.fi> wrote:
> From: Markus Kaukonen <markus.kaukonen.iki.fi>
> Subject: Re: [AMBER] QM/MM-MD binding energy
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Sunday, December 26, 2010, 5:23 PM
> Dear Ellac,
>
> Easiest way is to use DFTB+ (or some other QM software
> build in Amber).
> If QM part contains metals DFTB+ may be not a good idea (at
> least you
> need to test).
> In principle you follow tutorial 3
> http://ambermd.org/tutorials/advanced/tutorial3/
> with addition that you define QM region.
>
> It may be a good idea to read additionally some later
> publications
> from Ryde group as well, especially
> S. Genheden, U. Ryde (2010) "How to obtain statistically
> converged
> MM/GBSA results", J. Comput. Chem., 31, 837-846;
>
> Terveisin, Markus
>
>
> --www=http://www.iki.fi/markus.kaukonen
> --Markus.Kaukonen.iki.fi
> --office: N102 Nano building FIN-02015 TKK
> --home: Viinirinne 3 F 12, 02630 Espoo, FIN
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> --Suomessa. (Paimio 1998) ---
>
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Received on Sun Dec 26 2010 - 09:30:04 PST
