[gmx-users] Re: General query regarding MD simulation

Abhishek Acharya aacharya at iitk.ac.in
Sun Feb 17 18:07:46 CET 2013

>> Dear GROMACS Users.
>> Just out of curiosity, i would like to pose a general question here ( i
>> didn't have an idea of  any other suitable forum ). My protein active
>> site
>> has a GDP which is coordinated to a Mg ion. The Mg ion itself
>> coordinates
>> two water molecules and is held in position via non-bonded interactions
>> from two active site residues. For such a system, I could do two things:
>> 1. Do the charge calculation for GDP only and assume the charges of
>> other
>> active site constituents to be taken from the FF parameter library.
>> 2. As suggested by a a person I know, I can do the charge calculation of
>> the whole system including the Mg ion, water molecules and the residues.
>> The explanation was that since GDP is in coordination to Mg ion, the
>> effective charges would be different than on a GDP alone.
>> Can anyone explain which one of the above is a correct approach and why
>> ?
>> I somehow was not convinced by my co-workers explanation simply
>> considering the fact that for each of the amino acids in a protein the
>> charges and parameters are taken from the FF library. Going by the given
>> explanation, one should then resort to a charge calculation for the
>> whole
>> protein system.
> The charges and hence energies will be different for the GDP alone and
> for the coordinated GDP. If you want precise energetics, an adjustment
> is probably needed, but it is unlikely as trivial as recalculating the
> point charge using ab initio. If you are ok with more approximate
> description, than neglect the effect of Mg ion.
Dear Dr. Chaban.

Thanks for the insight. I'm not really sure though, how will the choice
affect my final results. I'm actually trying to look at the changes in the
protein in terms of backbone and sidechain movements as a result of GDP
and GTP binding to active site. The presence of Mg ion just complicates
My thoughts are like any other residue in protein, for Mg ion ang GDP/GTP
also, the standard charges should be able to govern the energetics and
hence the movements in the protein properly. Not sure, how much of a
difference would the change in charges due to polarization effects of Mg
ion make to the movements. I feel for my study it shouldn't make much of a
difference. I may be wrong though. Any thoughts ??

With Regards
Abhishek Acharya

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