Hi Brian
Thanks for your reply.
I read Amber12 will be released in few weeks, is it possible?
Otherwise I would be very interested in using the "modified" code, but
unfortunately
I'm not in contact with any developer.
Jacopo
2012/3/7 Brian Radak <radak004.umn.edu>:
> 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
> University of Minnesota - Twin Cities : Center for Integrative
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--
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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Received on Wed Mar 07 2012 - 23:30:02 PST
