r.py -p protein_pms.pdb -o protein_pms_t4p.pdb</pre>
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creating <code>protein_pms_t4p.pdb</code>. 
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<li>Next step is to truncate the protein, creating a scoop. This will enable us to solvate the protein in a droplet and thereby reduce the number of simulated particles. The command is
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<pre>python $PROTOMSHOME/tools/scoop.py -p protein_pms_t4p.pdb -l temp.pdb -o protein_scoop.pdb</pre> 
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The protein scoop is centred on the two ligand molecules and all residues further than 20 A are cut away. The 