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Table 1 Comparison of AMMP optimization methods for small molecules minimized with sp4 and sp5 force fields

From: AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening

    Optimization methods
Compound   Initial Energy Steepest descent Conjugate gradient BFGS Simplex GA
    Niter Emin Niter Emin Niter Emin Niter Emin Niter Emin
raloxifene sp4 121.08 20 86.72 1600 66.71 1500 75.89 80 102.24 300 69.97
  sp5 117.41 20 88.46 1000 71.65 1200 77.62 100 107.03 300 70.89
  RMSD    0.01   1.23   0.05   0.14   0.42
FDI sp4 119.61 30 74.02 200 66.14 1200 64.38 10 268.07 300 48.95
  sp5 116.89 30 75.48 300 67.94 1000 67.96 10 283.08 200 51.83
  RMSD    0.01   0.12   0.02   0.14   1.14
thymidine sp4 99.64 30 64.82 400 60.52 500 61.17 20 114.81 300 61.40
  sp5 95.78 20 68.49 200 64.29 1000 64.57 10 99.78 200 65.85
  RMSD    0.01   0.09   0.03   0.06   0.63
PR2 sp4 156.55 50 -5.22 300 -14.57 700 -13.58 10 78.01 200 -5.77
  sp5 155.04 50 1.11 300 -13.01 600 -11.77 20 72.18 200 -12.73
  RMSD    0.07   0.02   0.01   0.02   0.61
  1. The number of iterations needed to reach convergence (Niter) and the minimized energy (Emin in kcal/mol) and the RMSD values (in Å) between the optimized structures with sp4 and sp5 force fields are given.