On 01/25/11, ahmet yıldırım <[email protected]> wrote: > Hi, > > In my simulation, total charge of the system is a noninteger number (System > has non-zero total charge: 8.000004e+00). I neutralized it with 8 chlorine > atoms. > Then, grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr > > > Fatal error: > > moleculetype CU1 is redefined > is it some thing wrong? >
ions.itp defines molecule types for ions. Molecule types cannot be redefined. When you #included ions.itp GROMACS thought you were doing illegal redefinitions. Look back in the .top to find the original definitions, and then take suitable action. Mark > > > Below is the first and final version of the .top file: > > > First topol.top File > .... > [ molecules ] > ; Compound #mols > Protein_chain_P 1 > Protein_chain_L 1 > Protein_chain_H 1 > SOL 10 > SOL 127 > > SOL 157 > SOL 41779 > > > Final topol.top File > #include "ions.itp" > > [ molecules ] > ; Compound #mols > Protein_chain_P 1 > Protein_chain_L 1 > > Protein_chain_H 1 > SOL 10 > SOL 127 > SOL 157 > SOL 41771 > CL- 8 > > > > > > > > -- > Ahmet YILDIRIM > > >
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