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

Una Bjarnadottir una.bjarnadottir at ucd.ie
Mon Sep 11 13:00:00 CEST 2006


Dear Users,

I'm hoping for an answear on my problem with neutralizing my system adding 3 Cl ions with genion.  When 
running grompp after genion 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!  
When looking into the .ndx file atom 33000 is in 4 groups;  0 (system), 11 (non-protein), 14 (SOL) and 16 (other).  How can I change the group definitions and make sure the groups do not overlap and to be unique? 
 
It seems to be 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.

Please help because have not been able to fix the problem with related letters on the subject on the list.

Best regards, 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)








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