[gmx-users] water in protein itp file

[Mark Abraham]

raja wrote:
> 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.

Sorry, I don't understand the second half of this post. I appreciate 
that English isn't your native language, but can you express it in 
different words, please?

Mark