MacroModel Reference Manual - ISP

Chapter 4: Operation Codes45 [NEW] Do not delete dummy atoms for OPLS_2008. Dummy atoms are correctlyhandled in OPLS_2008.46 Don’t use fast vdw and hbd BMFF processing49 Don’t skip over structures that do not have all force field and solvation parameters.Stop when such a structure is encountered.50 GV, parsing of atom.typ file51 LV, parameter assignment55 [NEW] Don’t compare the connectivity of the input structure with the previousstructure, but treat it as chemically different from the previous structure.56 Don’t eliminate torsional interactions with V’s of 057 Always consider input structures to be distinct CT’s, not conformations. Thisimplies full interaction generation for each structure read in.58 GV, when which classes of params are updated (Bonded, VDW, Geom-dependent,solvation)59 GV, geom-dependent params & updating60 GV, .fld ALT and SEL processing61 GV, stretch interactions62 GV, bend interactions63 GV, torsional interactions64 GV, nonbonded interactions65 GV, bend-bend interactions68 GV, .fld atom-type equivalencing69 GV, .fld line-numbering & assembly of interactions; to .mmo70 GV, fixed atom interactions71 GV, parameters that change during FEP72 GV, atoms whose surface areas change during FEPMacroModel 9.7 Reference Manual 143