[gmx-users] GENION: Ions inside the protein

[Una Bjarnadottir]

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, 
index[8199]=11799

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