MacroModel Reference Manual - ISP

Chapter 4: Operation CodesLimitations:• If the EXNB opcode is used in the .com file, it must precede the BDCO opcode.• Use of the BDCO opcode automatically turns on DEBG flags 89 and 90. BDCO treats allatoms, including hydrogens, explicitly for the purposes of generalized Born solvation.However, if the file structure itself employs united atoms, such atoms are treated as unitedatoms. In other words, all atoms in the structure file are treated as they are for the purposesof generalized Born solvation in conjunction with BDCO.arg5Cutoff distance for charge-dipole interactionsThe default value is sqrt(cutes**3) where cutes is the electrostatic cutoff distance as per EXNB.arg6Cutoff distance for charge-charge interactionsThe default value is 9999999.0, which effectively includes all such interactions.These default settings typically yield shorter nonbonded pairlists than using residue-basedcutoffs and the same value for EXNB arg6.Related DEBG flags: 121, 126, 127, 128, 129.SOLV — SOLVation selectionSpecifies a solvation model (arg1) and a solvent (arg2), so that energy calculations include theapproximate effects of solvent.Solvation model 1 involved explicit solvent and is no longer supported.Models 2 and 3 read the appropriate solvent file named solvent_name.slv. The filewater.slv is available for models 2 and 3, while chcl3.slv and octanol.slv are availablefor model 3. MacroModel first looks in the local directory for the .slv file and, if it is notfound, looks in the $SCHRODINGER/mmshare-vversion/data directory.Solvent model 2 (arg1 = 2) is purely a surface-area-based model. We recommend model 3 forall computations where solvation energies are desired. Model 2 operates as described by Haselet al. [16]. See also Ooi et al. [17] for the parameter set given in water.slv. Solvent model 3provides a volume-based continuum model (the GB/SA model) for the electrostatic (polarization)component. [18]Using model 3, molecular electrostatics should be carried out with a constant dielectric treatmentand a low molecular dielectric constant (e.g., 1.0). Constant dielectric electrostatics willbe set automatically whenever solvent model 3 is used regardless of the default electrostaticequation selection in the force field file. EXNB should also be used with solvent model 3.MacroModel 9.7 Reference Manual 39