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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