MacroModel Reference Manual - ISP

Chapter 4: Operation Codes2 Use formal charges for mono-nuclear ions from the input structure file.3 Use formal charges for all atoms and bond orders for all bonds from the input structurefile.4 A combination of 0 and 3. Use charges, formal charges for all atoms and bondorders for all bonds from the input structure file.arg2Note:Treatment of sp3 CH n groups in GB solvation.Different charge sets can be specified for Coulombic and for GB solvation calculations.The charges used for Coulombic calculations are written to the first chargecolumn in the output file; the charges used for GB calculations are written to thesecond charge column.The only place in which this facility is currently used is in the treatment of sp 3 CH ngroups. When charges are assigned by the force field, then, for the purpose of GBcalculations only, charges on hydrogens in such a group are added to the charge on thecarbon, and the entire group is treated as a united atom.When reading an input file, the values in the first charge column are used for Coulombiccalculations and those in the second charge column are used for GB.0 (Default.) If all H atoms of an all-atom CH n group have zero charge, unite the groupfor GB calculations; otherwise, treat these H atoms explicitly. If a file is written outcontaining force-field charges, this default recaptures the force-field behaviorshould the file subsequently be read in with CHGF in effect.1 Never unite all-atom sp 3 CH n groups for GB.2 Always unite all-atom sp 3 CH n groups in GB. This allows a structure with equalcharge columns to be read in with CHGF and for the default behavior to be embodiedin the output; that is, the output will be suitable for reading with CHGF arg2=0.MacroModel 9.7 Reference Manual 43