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? 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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