MacroModel Reference Manual - ISP

Chapter 4: Operation Codes73 Don’t eliminate str/bend involving dummy atoms or zero-order bonds in FEP accumulation74 Exclude all str/bend terms from FEP accumulation78 Calculate normal modes only for SUBS atoms in LMOD and LLMOD calculations79 ATEQ, also consider noncyclic permutations of the ATEQ atoms81 GV, ATEQ, during csearch or mult MINI test for uniqueness82 GV, Comparing structures for uniqueness83 GV, MOLS and TORS moving-atom sets85 Use DRVPOL_OLD instead of DRVPOL; DRVPOL is faster for 1st derivs but has bad 2ndderivs. We use DRVPOL_OLD when we need 2nd derivs or when DEBG 85 is specified86 Use current rather than ideal str and bend distances in computing constant part ofanalytical GB radius87 GV, atom-wise solvation data to .mmo even if E(atom)=088 GV, read .slv solvation file and match its atoms to mol89 Don’t unite all-atom sp3 CHn groups for solvation90 Include explicit hydrogens in GB-radius calculation91 Use old (Hasel et al.) method for analytical surfaces92 GV, low-mode search (LMCS or LMC2)93 Turn off surface-area 3-body function94 GV, saddle point search. Also, write intermediate structures to output structure file.95 Use all-atom representation in surface calcs (assuming molecule actually has H’sand/or lone pairs)96 Ignore long range shells in numerical Born rad. calc97 GV, solvation energy calc98 GV, parameters for overlap array, solvation calc99 GV, analytical and numerical GB radii and Gpol values for fixed atoms144MacroModel 9.7 Reference Manual