MacroModel Reference Manual - ISP

Chapter 4: Operation Codesarg8Sparse Hessian cutoff value. Used with arg1=0 and arg1=4. (Similar toMINI/arg6).0 Default: 0.001>0 Other value to be used.Used with arg1=0, any H ij term that is less than arg8 in magnitude is excluded fromthe sparse Hessian representation. A single H ij element is the sum of a number of H ijterms coming from different interactions that map to the same coordinate indices (i,j). On the other hand, used with arg1=4, arg8 is interpreted the same way as arg6 inthe MINI command, i.e., only those elements of the Hessian matrix that are greaterthan arg8 are used in the sparse Hessian representation.MCMM — Monte Carlo Multiple MinimumMCMM [35, 36] is our recommended conformational search method. The input structure willbe modified by random changes in torsion angles and/or molecular position as specified by theTORS or MOLS commands. Ordinarily, whether a single structure or multiple structures appearin the input file, they will first all be read in, minimized and treated as if already found by theMCMM procedure. This allows a new search to be initialized from the output of a previoussearch, by using the output file of the old search as input for the new one. However, if thenecessary READ and MINI commands are placed within a BGIN/END loop, then a separatesearch is carried out for each input structure. This is called a serial search. For such serialcalculations, the AUTO opcode is also needed.The TORS command is used to specify dihedral angles to be varied; the MOLS command specifiesrelative positions of multiple molecules, as in an enzyme-substrate docking procedure. Inaddition, RCA4 commands and LIGB commands can be used to open rings and break ligandbonds, respectively, before performing torsional or relative molecular motion. CHIGcommands should be specified for ring-closure atoms as well as to retain chirality about othercenters. TORC commands may be used to hold double-bond configurations constant.The AUTO opcode can be used for automatic setup of any kind of MCMM calculation.Only unique structures will be retained, as in the MULT conformational searches. Use DEMX toset an energetic window to select low energy conformations. It is usually found that not allstructures converge in minimization during a conformational search. A MULT minimization ofthe output file is recommended to achieve convergence for the final result.While the default search method is random walk, we find that the usage-directed search (MCSSarg1=2) gives improved search performance.MacroModel 9.7 Reference Manual 101