Dear Jacopo
Thank you again for your reply on this question and sorry to come back.
Do you have by any chance the AMBER library/frcmod files needed for the
Magnesium-cationic dummy approach (developed by Warshel et al)? Or do you
know where can I find them?
Best wishes
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
>>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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
Received on Wed Nov 27 2013 - 03:30:02 PST
