MacroModel Reference Manual - ISP

Chapter 4: Operation Codesarg6Allowable interatomic approach distanceFraction of sum of van der Waals radii used as a closest atomic approach limit. If avan der Waals pair comes closer together than this as the result of an LMCS move,the move is rejected before minimization.0 Default: 0.25>0 Other fraction.arg7Minimum distance (Å)Same as LMCS, except that the default values are different, depending on arg3.0 Default: 3 (Å) for single mode, arg3 >= 01 (Å) for mixed mode, arg3 < 0>0 Other value to be used.arg8Maximum distance (Å)Same as LMCS, except that the default values are different, depending on arg3.0 Default: 6 (Å) for single mode, arg3 >= 02 (Å) for mixed mode, arg3 < 0>0 Other value to be used.LOOP — protein LOOP conformation generationLOOP is a conformational search method for protein loops that works in conjunction with theMINI opcode in a manner similar to MCMM.Given a single protein structure LOOP attempts to generate candidate loop conformations usingeither the specified loop from the protein structure provided or an alternate user specifiedsequence for the loop. LOOP rapidly generates a candidate structure with the appropriate bondlengths and angles. In addition, heavy atoms in this structure (i.e., atoms heavier thanhydrogen) will not approach each other more closely than a specified distance. These candidatestructures are then energy minimized and can be checked for uniqueness in a manner analogousto that for MCMM. A more general discussion of the use of LOOP is available in Chapter 13of the MacroModel User Manual.MacroModel 9.7 Reference Manual 93