MacroModel Quick Start Guide - ISP

Chapter 4: Conformational SearchesFigure 4.3. The Torsion Rotations panel (left) and the Molecule Trans/Rot panel (right).Torsion rotations indicate the torsions that are randomly rotated during the search. Allnon-trivial C-C and N-C bonds (except amide torsions) could be selected. It is only necessaryto choose the second and third atoms of the torsion.12. Choose Atoms from the Pick menu and select a few torsions from the structure in theWorkspace, (e.g., 1770/1771, 1779/1780, 1789/1790).13. Close the Torsion Rotations panel.14. In the CSearch tab, from the Search variables option menu choose Molecule Trans/Rot,then click Edit, to open the Molecule Trans/Rot panel (see Figure 4.3).The Molecule Trans/Rotation feature identifies molecules that are to be rotated and translatedrelative to each other. Only the ligand needs to be specified in this example.15. In the Workspace, select any atom in the ligand. Use the default minimum and maximumvalues.16. Close the Molecule Trans/Rot panel.To freeze the protein and start the job:This section uses the Substructure facility to freeze the receptor atoms that are within 6 Å ofthe ligand. MacroModel automatically ignores any remaining atoms in the computation.46MacroModel 9.7 Quick Start Guide