MacroModel Reference Manual - ISP

Chapter 4: Operation Codeswill actually be moved). If both ends are anchored by FXAT commands, then a ring closure(RCA4) command will be necessary. TORS and MOLS commands can be used together.arg1-2arg3-4arg5arg6Atom numbers specifying first torsionAtom numbers specifying second torsionMinimum dihedral angle variationA positive number in degrees (default: 0.0˚).Maximum dihedral angle variationA positive number in degrees (default: 180.0˚).TRES — Torsional RESolutionThis command may be used in the SPMC systematic pseudo Monte Carlo searches to alter theinitial resolution of the search around a particular torsion angle. This command must comeafter the TORS command.arg1-2arg3Atoms defining the torsional angleThese must have been listed already with a TORS command.Resolution for this angleThe value in degrees of the initial moves will be 360˚/arg3; thus arg3=3 (the default)gives 120˚ resolution.MOLS — variable MOLeculeS selectionThis command selects molecules to be independently rotated and/or translated during a conformationalsearch. It is used for configurational/conformational searches of complexes. In particular,given a docked bimolecular complex, MOLS can be used to translate and rotate the smallermolecule within the binding site of the larger one in order to explore possible binding geometries.MOLS and TORS commands can be used together; this allows the internal geometry of theseparate molecules to be explored together with the relative orientation. If there are N moleculesin the system, it suffices to specify N–1 of them in MOLS commands to ensure that all areadjusted.MOLS commands must come after TORS commands.During a search, random molecules are selected for motion. For each molecule, rotation aboutall three axes and translation along all three axes are performed by amounts selected randomly112MacroModel 9.7 Reference Manual