Hi, pdb2gmx -f 1LYD.pdb -water tip3p
Why is -water tip3p command ( tip3p water model) used? What the purpose? Afterwards, genbox command is already added to solvent water as the following: genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro Thanks -- Ahmet YILDIRIM
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