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【求助】建配体的力场，大家都用什么方法计算电荷？ 已有3人参与
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| 用ESP吗？ |
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2楼2010-04-14 15:17:37
bay__gulf
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小木虫(金币+0.5):给个红包，谢谢回帖交流
lei0736(金币+3):谢谢 2010-04-14 15:56
小木虫(金币+0.5):给个红包，谢谢回帖交流
lei0736(金币+3):谢谢 2010-04-14 15:56
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力场中的电荷并非原子真实的电荷, 而是根据某一计算方法得出的数值 放到整个力场参数中进行拟合得到的. 不同力场计算电荷的方法不同, 数值差别也很大 比如charmm 使用hf/6-31g* 基组下的Mullikin 电荷, 而amber 用的则是ESP. Methodologies for Developing the Partial Charges Now is a good time to discuss the determination of the partial charges appearing in the topology file. Two widely used force fields are CHARMM and AMBER – and they both use di?erent protocols to develop the partial atomic charges. CHARMM starts with the Mullikin charges and then strategically places a water molecule near any polar group. CHARMM’s charges are refined so that they best reproduce the interaction energy between the water and the polar group. To recreate these values, the partial charges of the polar group are then altered until this interaction energy is accurately replicated with the MD sim- ulations. Several concrete examples of this charge-fitting strategy are worked out in Ref. [7]. AMBER, on the other hand, begins with the ESP charges and then uses a program they distribute called RESP (for Restricted ESP). This charge-fitting scheme replicates the electrostatic potential at a distance out from the nucleus (much like the surface you built in the previous exercise) with only the atom centers having charge. Of course, the electrostatic surface generated using this methodisoftendegenerate; meaningtherecouldbemorethanonesetofcharges that would reproduce the potential surface. To resolve this issue, it is best to further restrict your potential surface by supplying it an initial set of charges for the program’s iterations, or further restrictions derived from chemical insight However they are generated, the importance of a good set of partial charges cannot be overstated. Much of the energy (and indirectly then, the behavior) of the system will be calculated using these values. |
3楼2010-04-14 15:30:37
4楼2010-04-16 16:02:48