Running Epik version 2.1209 Epik. Copyright Schrodinger, LLC. All rights reserved. Input file name: A.mae Output file name: B.mae Structure adjustment calculation requested. Target pH set to 7.000 pHt tolerance set to 1.000000e+00 Epik minmium tautomer probability set to 2.000000e-01 Adjusting structures for pH 7.000000e+00 and minimum probability 1.000000e-01 Solvent model name: water Using Incremental parameter file version: 1.0004 Jobcontrol is not being used for this specific Epik calculation. --------------------------- Processing Input Structure #1 Title: TEMP00000001 Calculated pKas Conjugate Atom Acid/Base pKa . . . . . . . . . . . . . . . . . . . . . . . Variation: 1 40 Conj_Acid 12.03 47 Conj_Acid 9.32 48 Conj_Acid 9.09 49 Conj_Acid 9.28 21 Conj_Base -2.23 pKa penalty: 0.01 kcal/mol Charging penalty: 0.00 kcal/mol Neutralization penalty: 0.01 kcal/mol Overall Penalty (tautomerization included): -0.00 kcal/mol Total Charge: 1 --------------------------- Processing Input Structure #2 Title: TEMP00000002 Calculated pKas Conjugate Atom Acid/Base pKa . . . . . . . . . . . . . . . . . . . . . . . Variation: 1 40 Conj_Acid 12.03 47 Conj_Acid 9.32 48 Conj_Acid 9.09 49 Conj_Acid 9.28 21 Conj_Base -2.23 pKa penalty: 0.01 kcal/mol Charging penalty: 0.00 kcal/mol Neutralization penalty: 0.01 kcal/mol Overall Penalty (tautomerization included): -0.00 kcal/mol Total Charge: 1 ---------------------------