MacroModel Reference Manual - ISP

Chapter 4: Operation Codesarg3The maximum total number of failed attempts at generating a new loopconformation.If this number is exceeded then the loop construction process fails andMacroModel terminates with an error message.Default: 100,0002 Geometric parametersarg5The closest permissible approach of a loop heavy atom to a heavy atomwithin the rest of the protein.Default: 2 Åarg6Related DEBG flags: 555The closest permissible approach of a loop heavy atom with another loopheavy atom.Default: 2 ÅARPK — ARPacK parametersThis opcode applies to LMC2, VBR2, and LTNCG (MINI arg1=11)The ARPACK package was developed by Danny Sorensen, Richard Lehoucq, Chao Yang, andKristi Maschhoff at Rice University [33, 34]. Instead of attempting to solve a huge eigenproblemdirectly, ARPACK solves it indirectly by solving a series of small problems of muchlower dimensionality and references the huge matrix only implicitly through its product withsome vectors. ARPACK is ideally suited for LLMOD calculations, because direct calculationof the low-mode eigenvectors of a huge Hessian matrix of a protein molecule is prohibitive.Instead, LLMOD utilizes ARPACK to compute the low-mode eigenvectors indirectly. TheARPK command allows a user to fine tune ARPACK parameters. Note that the VBR2 commandalso uses ARPACK to calculate vibrational modes.DEBG 999 can be used to provide greater verbosity for ARPK.arg1Select a method to calculate Hessian × vector0 Default: The Hessian is calculated analytically, but it is stored in a sparse vector representation,not in matrix form, and allows for fast matrix-vector multiplication,which scales only linearly with the number of dimensions. This is the recommendedmethod.1 H×v is calculated by a finite difference formula based on gradients (see Kolossváryand Keseru [29]). This method does not need second derivatives. It is fast, but isoften unstable and converges only very slowly.98MacroModel 9.7 Reference Manual