[gmx-users] genion doesn't recognize SOL in top file

sunyeping sunyeping at aliyun.com
Thu Oct 17 19:01:46 CEST 2013

Dear Gromacs users,
I am trying to add ions to my system using:genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -np 8

but it returns a error message saying:

Fatal error:
No line with moleculetype 'SOL' found the [ molecules ] section of file 'topol.top'

I checked the topol.top file, but SOL is indeed under [ molecules ] section:

[ molecules ]
; Compound        #mols
Protein_chain_A     1
Protein_chain_B     1
DRG                 1
SOL             86574

I know it problem has been disscussed here before, but I cann't fix it out with the avialable information. Could you help me with it?

Thanks in advance.
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences

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