[gmx-users] Partial charge distribution for metal ligating atoms

raja raja_28 at fastmail.us
Wed Nov 29 04:34:15 CET 2006

Thanks Mark for your valuable suggestions and dedicating your valuable
time for me.

On Wed, 29 Nov 2006 00:47:33 +1100, "Mark Abraham"
<Mark.Abraham at anu.edu.au> said:
> raja wrote:
> > Thanks Goette for your mail. So system neutrality is restored as per
> > your advice but individual residue will deviate from its integer value
> > (formal charge), won&#8217;t violate anything? 
> A residue is an artificial grouping construct. There's nothing magical 
> about them. Like I said before, you want neutral charge groups for a 
> well-formed simulation with cut-offs. They are the relevant artificial 
> grouping construct.
> > I remember once I read the
> > lines of individual residues' partial charge should be an integer from
> > gromacs manual, I really took some time to search it in manual to refer
> > that line in this mail, but I could not find it.
> Try reading the section reference I gave you earlier.
> > But I am also using
> > Autodock (Docking tool), where the non-integral charge on residue based
> > is not allowed. May be I overlapped these two programs concept of
> > partial charges!
> So redefine what a residue means!
> Mark
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