[gmx-users] water in protein itp file

[raja]

Dear Mark,
Thaks for your replies and I end this discussion with this.

B.Nataraj



On Wed, 15 Nov 2006 11:51:37 +1100, "Mark Abraham"
<Mark.Abraham at anu.edu.au> said:
> 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
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-- 
  raja
  raja_28 at fastmail.us

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