[gmx-users] charge in genbox

Justin A. Lemkul jalemkul at vt.edu
Wed Jun 18 22:09:28 CEST 2008

I've seen genbox report that the charge on the system is 0 as well, even 
if my protein is charged.  I don't think it means anything, but it is 
strange that it comes up.  It's never caused a problem for me, so I 
guess that's why I never investigated it further!


Serena Leone wrote:
> Hello 
> 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
> Serena
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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