[gmx-users] genion causing atom to be in multiple T-Coupling groups

[Una Bjarnadottir]

Dear Users,

I'm trying to neutralize my system adding 3 Cl ions with genion and when 
running grompp again with the new generated .gro file I get this error:
Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1)

which is the last water atom (total in system 33003) and groups 15 and 1 
are Cl and protein groups if I on the other hand do not neutralize the 
system the run goes fine!  So there is something wrong with how the 
genion works for me.  I followed the tutorial and chose the SOL group 
and water molecules were replaced by the Cl ions.  Than I modifyed the 
.top file and took 3 sol molecules and added the 3 ions.
_*
*_Best regards for any help, Una Bjarnadottir
_*
.top before:
*_; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_E           1
Protein_I            1
Protein_A          1
SOL             9719
_*.top after*_
; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_E           1
Protein_I            1
Protein_A          1
SOL             9716
CL-                    3

_*These are my commands:*_
    #
    #Run grompp
    #
    emfile_mdpfile='em.mdp'
    emout='em_out.mdp'
    structure_file='em.tpr'
    os.system('/usr/local/bin/grompp -f '+emfile_mdpfile+ ' -po ' 
+emout+ ' -c ' +water_grofile+ ' -o ' +structure_file+ ' -p ' +topologyfile)

    #
    #Run genion
    #
    ion_out='ion.gro'
    os.system('/usr/local/bin/genion -s '+structure_file+ ' -o ' 
+ion_out+ ' -nname Cl -nn 3')

    #
    #Run grompp
    #
    structure_file_after_genion='em_genion.tpr'
    os.system('/usr/local/bin/grompp -f '+emfile_mdpfile+ ' -po ' 
+emout+ ' -c ' +ion_out+ ' -o ' +structure_file_after_genion+ ' -p ' 
+topologyfile)