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

[Ashima]

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’

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




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