[gmx-users] atoms in .top and .gro dont match

Mark Abraham Mark.Abraham at anu.edu.au
Tue Apr 18 16:08:47 CEST 2006

arunima singh wrote:
> I am simulating lysozyme 1AKI.pdb in water box gor normal mode analysis. 
> The energy minimization and position restrained MD are running correctly 
> but when doing grompp for normal mode it shows the error "stoms in .top 
> anf .gro dont match(Cl-HW2)"
> I dont understand what is going wrong. please help.

You haven't said this, but my guess is that you've used genion to add a 
chloride ion after your position restrained MD, and haven't updated the 
[ molecules ] section of your .top file accordingly. In any case, the 
molecules section must have the same molecules in the same order as the 
.gro file, so see where they differ and fix it.


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