Dear users, I am using gromacs 4.5.3. Initially I removed ligands from pdb file. Then I started to simulation .I met such a problem ( last error) after I added ions. What could be the problem? pdb2gmx -f withoutligand_xxx.pdb editconf -f conf.gro -bt cubic -d 1.0 -o box.gro genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
*Fatal Error:* System has non-zero total charge: -1.500000e+01 genion -s em.tpr -o solvated.gro -pname NA+ -np 15 -g em.log select: Group 13 (SOL) grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr *Fatal error:* number of coordinates in coordinate file (solvated.gro, 106473) does not match topology (topol.top, 106518) *topol.top:* .. [ molecules ] ; Compound #mols Protein_chain_A 1 Protein_chain_B 1 SOL 185 SOL 143 SOL 33723 NA 15 -- Ahmet YILDIRIM
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