[gmx-users] genion

T.A.Wassenaar T.A.Wassenaar at rug.nl
Tue Mar 1 09:35:56 CET 2005


Probably genion placed solvent inside the protein, and you 
used genion without the -random option. In that case it 
places the ion where the potential is most favorable, 
which will usually be inside the protein.

Either delete the solvent within the protein, or try the 
option -random with genion.

Hope it helps,


On Tue, 01 Mar 2005 13:59:49 +1100
  Dallas Warren <dallas.warren at vcp.monash.edu.au> wrote:
>>I used "genion" to add a Cl- to neutarlize my system. But 
>>I just noticed
>>that the Cl- was put within the protein. Is it supposely 
>>like this???
> Did you use it in replacing a water molecule?
> It should just shove it where it fits, randomly around 
>the box.  I suspect if you ran it again you will find 
>that it puts it somewhere else.
> Catch ya,
> Dr. Dallas Warren
> Lecturer
> Department of Pharmaceutical Biology and Pharmacology
> Victorian College of Pharmacy, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at vcp.monash.edu.au
> +61 3 9903 9083
> --------------------------------------------------------------------------
> When the only tool you own is a hammer, every problem 
>begins to resemble a nail.

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