[gmx-users] General query regarding MD simulation.

Abhishek Acharya aacharya at iitk.ac.in
Fri Feb 15 19:29:20 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.

Thanks in advance
With Regards
Abhishek Acharya

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