[gmx-users] GENION: Ions inside the protein

Una Bjarnadottir una.bjarnadottir at ucd.ie
Tue Oct 10 17:08:59 CEST 2006

Dear users,

In some of my simulations after neutralizing the systems with genion 2 
of the ions were inside the active site cleft of the protein. 
In the discussion on the list it was commented to either delete the 
solvent within the protein which I did I deleted the water molecule 
(11798) and gave genion that index file as input but than this error came:

Fatal error: The solvent group is not continuous: index[8198]=11797, 

I don't want to use the -random command in genion if possible because in 
none of the other simulations I have used it.

Is there any other way to delete the solvent within the protein did I 
misunderstand that so those water molecules will not be replaced?

Best regards, Una Bjarnadottir

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