Manzoni Francesco, Söderhjelm Pär
Department of Theoretical Chemistry, Chemical Center, Lund University, P.O. Box 124, 221 00, Lund, Sweden,
J Comput Aided Mol Des. 2014 Mar;28(3):235-44. doi: 10.1007/s10822-014-9733-3. Epub 2014 Mar 1.
Hydration free energy calculations are often used to validate molecular simulation methodologies and molecular mechanics force fields. We use the free-energy perturbation method together with the AMOEBA polarizable force field and the Poltype parametrization protocol to predict the hydration free energies of 52 molecules as part of the SAMPL4 blind challenge. For comparison, similar calculations are performed using the non-polarizable General Amber force field. Against our expectations, the latter force field gives the better results compared to experiment. One possible explanation is the sensitivity of the AMOEBA results to the conformation used for parametrization.
水合自由能计算常用于验证分子模拟方法和分子力学力场。作为SAMPL4盲测挑战的一部分，我们使用自由能微扰方法结合AMOEBA可极化力场和Poltype参数化协议来预测52种分子的水合自由能。为作比较，使用非可极化的通用琥珀色力场进行了类似计算。出乎我们意料的是，与实验结果相比，后一种力场给出了更好的结果。一种可能的解释是AMOEBA结果对用于参数化的构象敏感。
