[gmx-users] genion question

Mark Abraham mark.abraham at anu.edu.au
Tue Dec 12 00:57:53 CET 2006

> Hi Guys,
> I have a question.  I am using genion to add two ZN2+ ions to a protein
> that
> already has two.  I thought I would just use genion with –np 2.  However
> it
> seemed to recognize that there were already two in the file and added
> none.
> So instead I used the parameter –np 4.  This seemed to add two, for a
> total
> of four, which I wanted.  However sometimes it seems to add two too many!
> Am I understanding the proper use of the –np parameter?

If it "seemed" to add two too many, then the most likely cause was that
you had fewer ions in your input structure than you thought you had. You
should check out the man page for genion, and consider using -pq.


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