[gmx-users] Adding ions

mohammad r mohammad.r0325 at yahoo.com
Sun May 22 15:22:52 CEST 2016

 Hi GROMACS users,
I solved my proteinin a defined box of water. Now I want to add ions to neutralize thesystem. But when I use “grompp -f ions.mdp -c solv.gro -pgromacs.top -o ions.tpr” to generate the .tpr file I receive thiserror :
Fatal error:No such moleculetypeSOLFor more informationand tips for troubleshooting, please check the GROMACSwebsite athttp://www.gromacs.org/Documentation/Errors
in the .gro and .topboth the SOL exists. I don not know what the problem is exactly.Also, before thiscommand I defined the box and solved the proteins by these commands: 
gmx editconf -fgromacs.gro -o protein.gro -c -box 8gmx solvate -cpprotein.gro -cs spc216.gro -o solv.gro -p gromacs.top
Thank you, Mohammad.

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