MacroModel Reference Manual - ISP

Chapter 5: MINTAtion (25,000 total per conformation). Non-adaptive Monte Carlo integration is applied in“soft-mode” space spanned by the first 50 low-frequency vibrational modes. The rest ofthe modes are integrated using the fast analytical MINTA method. The temperature is setto 300 K. The size of the integration volume (box) in “soft-mode” space is determined bythe lesser of 1 Å and three-times the standard deviation (see arg6 and arg7 of the MINTAcommand description above).• n.log where n stands for the numbers 1-7. These logfiles are the logfiles of the MINTAcalculations 1-7.Based on the ‘Gtotal’ values in the logfiles, the MINTA calculation on cyclononaneyields the following result:Order of cyclononane conformations based on (MM2) steric energy:__ E ∆E (kJ/mol)------------------1. 97.86 0.00 global minimum steric energy2. 101.00 3.143. 101.10 3.244. 107.16 9.305. 111.10 13.246. 121.59 23.737. 141.13 43.27Order of cyclononane conformations based on (MM2) MINTA free energy:G ∆G (kJ/mol)-----------------1.(2.) 481.24 0.702.(3.) 481.36 0.823.(1.) 480.54 0.00 global minimum free energy4.(4.) 484.81 4.275.(5.) 489.32 8.786.(6.) 499.58 19.047.(7.) 521.48 40.945.6.2 GlucoseIn the subdirectory glucose the necessary files are provided for running an anomeric freeenergycalculation on glucose using the AMBER* force field and GB/SA continuum solvationfor water. In this example, we are looking at the total free energy of each of two sets of conformations(one set for the α anomer, and one for the β anomer). Note that the α anomer and βMacroModel 9.7 Reference Manual 175