Hi Jacopo,
The AM1/d-PhoT parameters from Nam, et al. and magnesium parameters from
Imhof, et al. are available as the defaults for "AM1D" in SQM and AMBER
QM/MM. However, this is in the *development* version of AMBER11; I am not
sure if they are in the version you have. My initial impression is that
use of the d-orbital code has not made its way outside of the
York/Walker/Case circle of users. These changes will almost definitely be
released "soon" as part of AMBER12. I'm not a direct part of this
development project so this promise is somewhat empty, perhaps Taisung will
read this and give an official answer.
Regards,
Brian
On Wed, Mar 7, 2012 at 6:17 AM, Jacopo Sgrignani <sgrigna.sissa.it> wrote:
> Dear all
> I'm working with a magnesium containing enzyme and I would like to try
> QM/MM MD with a semiempirical method.
> I found two paper about an AM1 parameterization that seems good for my
> system.
>
> Kwangho Nam,Qiang Cui,Jiali Gao,and Darrin M. York. Specific Reaction
> Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer
> Reactions: H, O, and P Atoms. J. Chem. Theory Comput., 2007, 3 (2),
> pp 486–504
> and
> Imhof, P.; Noé, F.; Fischer, S.; Smith, J. C. J. Chem. Theory Comput.
> 2006, 2, 1050– 1056
>
> Actually, these parameters have been successfully used by the York
> Group also in a recent work, J. Chem. Theory Comput., 2011, 7 (1), pp
> 1–3.
>
> How can I use this parameter in amber? Is it the possibility to add
> this parameters?
>
> Thanks a lot
>
> Jacopo
>
> --
> Jacopo Sgrignani PhD
> CNR-IOM-Democritos National Simulation Center
> c/o International School for Advanced Studies (SISSA/ISAS)
> via Bonomea 265,
> 34136
> Trieste
> Italy
> email: sgrigna.sissa.it
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
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Received on Wed Mar 07 2012 - 08:00:02 PST
