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

Mark Abraham Mark.Abraham at anu.edu.au
Tue Nov 28 14:47:33 CET 2006

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’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!


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