On 23/11/2010 8:35 PM, ahmet yıldırım wrote:
Hi,
pdb2gmx -f 1LYD.pdb -water tip3p
Why is -water tip3p command ( tip3p water model) used? What the purpose?
This chooses the water model embedded in the system topology written by
pdb2gmx.
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
This generates the coordinates of the water molecules, but doesn't know
or care what model the .top employs.
You need both a model and coordinates to do a simulation.
Mark
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