<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:arial, helvetica, sans-serif;font-size:8pt;color:#000000;"><div>Hello,</div><div><br></div><div><br></div><div> 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.</div><div><br></div><div>Thanks, Marc</div><div style="position:fixed"></div>
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