MacroModel Reference Manual - ISP

Chapter 4: Operation Codesarg4The number of loop conformations to generate0 Default: 100arg5The maximum number of loop conformations to keep0 Default: 10000arg6Allowable interaction approach distanceIf a given pair of atoms is closer than arg6 times the sum of their van der Waals radiiafter loop generation just prior to minimization then the structure is rejected andanother loop structure is generated.0 Default: 0.25arg7−1Automatic generation of COMP and CHIG atom lists for the loopDon’t generate COMP or CHIG commands for the atoms in the loop.0 Automatically generate COMP commands for the heavy atoms in the loop and CHIGcommands for atoms in the loop.1 Automatically generate COMP commands and CHIG commands for all the atoms inthe loop.2 Automatically generate COMP commands for the heavy atoms in the loop and do notgenerate any CHIG commands.3 Automatically generate COMP commands for all the atoms and do not generate anyCHIG commands.Related DEBG flags: 555LPOP — LooP OPtionsLPOP provides a means to modify some of the parameters related to protein loop generationwith the LOOP opcode. If no LPOP commands are provided the default values for the parametersare used. Multiple LPOP commands (e.g., with different arg1 values) may be used. It is notexpected that these parameters would need to be modified from their default values undernormal conditions so typically one would not need to include a LPOP command in the .comfile.96MacroModel 9.7 Reference Manual