Re: [AMBER] QM/MM simulation

From: Brian Radak <>
Date: Wed, 25 Apr 2012 09:11:33 -0400

Hi Soma,

To my knowledge, there are very few semi-empirical QM methods calibrated
for Fe in a biological context, let alone implemented in AMBER. PM6 is a
possible exception, but I don't believe it is implemented in AMBER with
d-orbitals. SCC-DFTB (or perhaps DFTB3, I can't remember) also has an Fe
parameterization, but I don't know if it requires d-orbitals or is
otherwise properly supported in AMBER.

Our group recently had a discussion concerning Fe and, due to the exotic
spin states needed (AMBER can only handle singlets), it was decided that
really the only possible route was through *ab initio* methods. As such,
you might consider looking into the new Extern options.


On Wed, Apr 25, 2012 at 8:19 AM, ashwini gupta <> wrote:

> Dear AmberUsers,
> I am trying to run a QM/MM simulation for a metal active site and the metal
> is Fe. However, when i read through amber9 tutorial i see that none of the
> QM theories defined in amber9 support Fe. The available theories as
> described in the tutorial are
> MNDO: H, Li, Be, B, C, N, O, F, Al, Si, P, S, Cl, Zn, Ge, Br, Sn, I, Hg, Pb
> AM1: H, C, N, O, F, Al, Si, P, S, Cl, Zn, Ge, Br, I, Hg
> PM3: H, Be, C, N, O, F, Mg, Al, Si, P, S, Cl, Zn, Ga, Ge, As, Se, Br, Cd,
> In, Sn, Sb, Te, I, Hg, Tl, Pb, Bi
> PDDG/PM3: H, C, N, O, F, Si, P, S, Cl, Br, I
> PDDG/MNDO: H, C, N, O, F, Cl, Br, I
> PM3CARB1: H, C, O
> DFTB/SCC-DFTB: H, C, N, O, S, Zn
> None of them support element. Can i use the theory which support Zn (for
> eg: MNDO or PM3). Is there any specific reason why Fe has not been
> included. What are the other options to go ahead with FE.
> Thanks and Regards
> Soma
> _______________________________________________
> AMBER mailing list

================================ Current Address =======================
 Brian Radak                                             :     BioMaPS
Institute for Quantitative Biology
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Received on Wed Apr 25 2012 - 06:30:03 PDT
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