[gmx-users] Manual Counterion Placement

Marc Charendoff mcharend at sbcglobal.net
Mon Sep 19 01:46:47 CEST 2011


        I  would like to manually place a counterion into my system with the 
genion command for which I am pretty sure I will need an index file. My question 
is how to properly select the specific water atoms / or SOL residue(?)  number 
 (that I get from my pdb or gro file)  so that it comes up as an option when I 
run genion. I looked at the make_ndx options, but they weren't too clear to me. 
Guidance appreciated.

Thanks, Marc
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