[gmx-users] Partial charge distribution for metal ligating atoms
Mark.Abraham at anu.edu.au
Tue Nov 28 14:47:33 CET 2006
> 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’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
> 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!
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