Hi,<br><br>pdb2gmx -f 1LYD.pdb -water tip3p<br><br>Why is -water tip3p command ( tip3p water model) used? What the purpose?<br><br><br>Afterwards, <span lang="en"><span title="">genbox command is already added to solvent water</span></span> as the following:<br>
<br>genbox −cp box.gro −cs spc216.gro −p topol.top −o solvated.gro<br><br>Thanks<br><br clear="all"><br>-- <br>Ahmet YILDIRIM<br>