From: Michele Formica (michele.formica.ph_at_gmail.com)
Date: Thu May 23 2013 - 07:40:44 CDT

Hello there everybody,
I need to solvate my NP in a box of water. I created the *.psf and *.pdb
file for the NP and the water box and followed the procedure here:

https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---various-tips-tricks

but there's still water in the gold core of my NP.

Two questions:

What should I write where it says: [a b c alpha beta gamma} ?

What should I write where it says: set sel [atomselect $combined "not
(same fragment as (exwithin $mindist of solute))"] ?

Thanks, regards