MacroModel Reference Manual - ISP

Chapter 4: Operation Codes1 The current input filename.mae file.arg2Disposition of intermediate output0 Discard; at the end of program execution, there will be a single output file, typicallynamed filename-out.mae, that contains only the output generated following the lastRWND command.1 Keep intermediate output in separate files, typically named filename.ou1, filename.ou2,etc. The final output appears in filename-out.mae.2 Keep all intermediate output, together with final output, in a single file, typicallynamed filename-out.mae.4.4 Hydrogen Addition and DeletionHADD — Hydrogen ADDAdd hydrogens and lone pairs to a structure. This command must come immediately after theREAD command if it is used.arg1Control0 Hydrogens added to all atoms of structure1 Hydrogens added to all non-carbon atoms of structureHDEL — Hydrogen DELeteHydrogen delete, opposite of HADD. This command must come immediately after the READcommand if it is used. This command deletes lone pairs and hydrogens attached to carbonsonly.4.5 Energy CalculationELST — Energy LiSTingCalculate energy of current structure and dump Energy LiSTing to one or more output files.Can be used within a BGIN/END loop to compute energies of all structures in a file. ELSTcannot be used with the MC conformational searching commands (MCMM, MCSM).By default, very close nonbonded atomic pairs will be separated before the energy calculationis done. To override this, specify DEBG flag 33. By default the first 100 such pairs encounteredMacroModel 9.7 Reference Manual 45