[gmx-users] charge in genbox

Serena Leone sleone at rics.bwh.harvard.edu
Wed Jun 18 21:50:03 CEST 2008


I've recently started using Gromacs, and I'm trying to model a charged
polypeptide. I built it either with maestro or pymol, I generated
the .top and .gro, and according to the topology files it has the
expected charge (+5). When I try to generate the water box, after
running genbox and before running genion, I notice that the total system
charge is reported to be 0. Does anybody knows what I am overlooking?
Thanks a lot

Have a great day


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