[gmx-users] GROMACS Error

Asma Mushtaq ashima.ashia at gmail.com
Fri Feb 8 19:40:55 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

and choose group 15 (SOL), the error is

Fatal error:

No line with moleculetype 'SOL' found the [ molecules ] section of file

but 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

ATQwild              1

SOL                  24504

Please let me know how to rectify the problem



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