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

Dr. Vitaly Chaban vvchaban at gmail.com
Fri Feb 15 22:47:08 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.

Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark

More information about the gromacs.org_gmx-users mailing list