[gmx-users] genion error { problem only with PROTEIN-LIGAND complex} - No line with moleculetype 'SOL' found the [ molecules ] section of file ‘topol.top’

Ashima ashima.ashia at gmail.com
Sat Feb 9 07:36:17 CET 2013

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 

I am able to add the ion easily to a protein or protein-peptide complex by
using the above command line where I replace the 6 SOL with 6 CL ions. 

But when I use the above command line for Protein-Ligand complex 
and choose group 15 (SOL), the error is 
Fatal error: 
No line with moleculetype 'SOL' found the [ molecules ] section of file

when I check the ‘topol.top’ file I found there are 24504 SOL molecules
My topology file looks like this 
; Include water topology 
#include "amber99sb.ff/tip3p.itp" 
; Position restraint for each water oxygen 
[ position_restraints ] 
;  i funct       fcx        fcy        fcz 
   1    1       1000       1000       1000 
; Include topology for ions 
#include "amber99sb.ff/ions.itp" 
[ system ] 
; Name 
[ molecules ] 
; Compound        #mols 
Protein_chain_A      1 
Ligand               1 
SOL                  24504 

Please let me know how to rectify the problem 

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