[gmx-users] water in protein itp file

raja raja_28 at fastmail.us
Tue Nov 14 06:04:38 CET 2006

Dear Mark,
Well and thanks again, QM-MM is a good option, as you said for analyzing
the energetic of water ligating process. But my case not concerning to
that process, rather study a system consists of a macromolecule as a
whole, where this water bound zinc is a part of it. If this is a case of
QM-MM to be done for this process, then how it is encouraged for other
protein residues, like His NE2, Asp OD, GLU OD, atoms making similar
interaction with metal ion to use harmonic bond constraints. When it is
true and possible for amino acid ligating atoms, why it is not for
oxygen atoms from a water molecule.

With thanks!

On Tue, 14 Nov 2006 15:22:30 +1100, "Mark Abraham"
<Mark.Abraham at anu.edu.au> said:
> raja wrote:
> > Dear Mark,
> > Thanks for your immediate reply and good solution. But until before
> > yours this mail, I was thinking that inclusion of water and restraining
> > them with metal ion is a very common happening in MD. Since in my short
> > spell of molecular modeling and drug design experience, I have found
> > almost 75% of the drug targets are metalo-enzyme and if you can still
> > probe its active site, can invariably find water ligating with metal in
> > most of the cases (Say 90%). This water bound form is present until an
> > external ligand or drug replace and ligate with metal ion for enzyme
> > inhibition process. I am really wondering a case, which I think quite
> > common, is not able to depict easily in gromacs. I am so interested to
> > extend this topic, how other gromacs users depict this scenario in their
> > simulation.... Am I doing any thing stupid, I doubt myself?
> If you actually want accurate energetics, you should really be looking 
> at QM-MM simulations, which are a whole different ballgame in complexity 
> and cost. I understand GROMACS does interface with GAMESS for these 
> kinds of simulations, but that's where my knowledge ends. You should 
> definitely do some literature reading on QM-MM simulations and see what 
> software people have actually been using successfully. Probably, you 
> should use that, rather than trying to make GROMACS do the job.
> Mark
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  raja_28 at fastmail.us

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