[gmx-users] genion error - No line with moleculetype 'SOL' found the [ molecules ] section of file ‘topol.top’

[Asma Mushtaq]

Dear All,



I need to add 6 CL ions to make the system neutral but when I type the
command line



genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -nn 6



and choose group 15 (SOL), the error is



Fatal error:

No line with moleculetype 'SOL' found the [ molecules ] section of file
‘topol.top’



but when I check the ‘topol.top’ file I found there are 24504 SOL molecules
present.



My topology file looks like this



; Include water topology

#include "amber99sb.ff/tip3p.itp"



#ifdef POSRES_WATER

; Position restraint for each water oxygen

[ position_restraints ]

;  i funct       fcx        fcy        fcz

   1    1       1000       1000       1000

#endif



; Include topology for ions

#include "amber99sb.ff/ions.itp"



[ system ]

; Name

Protein



[ molecules ]

; Compound        #mols

Protein_chain_A      1

Ligand               1

SOL                  24504



Please let me know how to rectify the problem



regards,



Ashima