Dear Jacopo
Thanks so much for your reply.
But if one does not look at the chemistry at the catalytic site
(coordination of ions, transition states, ligand binding etc),
but the overall conformation of the protein, the choice of +2
value shouldn't too much of a problem.
Is this correct?
George
> Dear George
> there are several approaches to simulate Mg2+ in proteins.
> In my experience using a simple 2+ charge can produce strong changes
> in the Mg2+ coordination sphere.
> Also using a "arbitrary" reduction of 0.5 of the charge is not a good
> idea.
>
> One recipe was proposed in Dal Peraro et. al. J Struct. Biology,
> 2007, 3, 444. It is based on charge corrections derived using Bader
> Atoms in Molecule approach.
> Another smart way is using the dummy cation approach developed by
> Warshel and coworkers (Oelschlaeger, P.; Klahn, M.; Beard, W. A.;
> Wilson, S. H.; Warshel, A. J. Mol. Biol. 2007, 366, 687? 701).
> I compared this last approach with the geometries sampled in
> QM(DFT)/MM simulations (Sgrignani and Magistrato J. Phys. Chem B.
> 2012) and it seems to work well.
> Notably the dummy cation approach does not require any additional
> calculations, you only need libraries for amber.
>
> Regards
>
> Jacopo
>
>
>
> 2013/10/4, George Patargias <gpat.bioacademy.gr>:
>> Hello
>>
>> Sorry if this is trivial. Is there an issue with the +2 charge of Mg in
>> AMBER FF or in other FFs? I mean, is there evidence from simulations
>> that
>> the use of +2 value will cause artifacts such as too strong interactions
>> between Mg and negatively charged residues Asp, Glu?
>>
>> If this is the case would an ad hoc solution like the reduction of Mg
>> charge to, say, +1.5 have any point?
>>
>> Many thanks in advance for any clue on this.
>>
>> Best wishes
>> George
>>
>>
>> Dr. George Patargias
>> Postdoctoral Researcher
>> Biomedical Research Foundation
>> Academy of Athens
>> 4, Soranou Ephessiou
>> 115 27
>> Athens
>> Greece
>>
>> Office: +302106597568
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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>
Dr. George Patargias
Postdoctoral Researcher
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27
Athens
Greece
Office: +302106597568
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Received on Fri Oct 04 2013 - 06:00:23 PDT
