MacroModel Quick Start Guide - ISP

Contents2.10.2 Filtering by Sorting.......................................................................................... 27Chapter 3: Energy Calculation and Minimization ........................................... 293.1 Current Energy Calculations ................................................................................ 293.1.1 Calculating the Gas-phase Potential Energy .................................................... 293.1.2 Investigating Force Field Interactions................................................................ 313.1.3 Calculating the Solution-phase Current Energy................................................ 323.2 Energy Minimization ............................................................................................... 323.2.1 Energy Minimization of a Single Structure........................................................ 333.2.2 Comparing Structural Results by Superposition ............................................... 343.2.3 Energy Minimization of Multiple Structures....................................................... 353.2.4 Energy Minimization of a Substructure ............................................................. 37Chapter 4: Conformational Searches ..................................................................... 414.1 MCMM Search .......................................................................................................... 414.2 Serial MCMM Conformational Search.................................................................. 424.3 Serial Low-Mode Search ........................................................................................ 434.4 Ligand Conformational Search with a Frozen Receptor .................................. 444.5 Substructure Conformational Search with Automatic Setup.......................... 474.6 Large-Scale Low-Mode Conformational Search ................................................ 50Chapter 5: Other Calculations ..................................................................................... 515.1 Embrace .................................................................................................................... 515.2 Molecular Dynamics ............................................................................................... 535.3 Creating Energy Profiles From Coordinate Scans ............................................ 555.3.1 Performing a Coordinate Scan Calculation ....................................................... 555.3.2 Analyzing the Results of the Coordinate Scan.................................................. 575.4 MINTA Prediction of Free Energy ......................................................................... 585.5 Partition Coefficient Between Two Solvents ...................................................... 595.6 Analysis of Molecular Structure With XCluster ................................................. 61ivMacroModel 9.7 Quick Start Guide