| 查看: 1116 | 回复: 3 | |||
| 当前主题已经存档。 | |||
[交流]
【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
|
|||
| 用ESP吗？ |
回复此楼» 猜你喜欢
国家基金申请书模板内插入图片不可调整大小?
已经有9人回复
-
退学或坚持读
已经有20人回复
-
免疫学博士有名额，速联系
已经有14人回复
-
面上基金申报没有其他的参与者成吗
已经有4人回复
-
多组分精馏求助
已经有6人回复
-
国家级人才课题组招收2026年入学博士
已经有6人回复
2楼2010-04-14 15:17:37
bay__gulf
金虫 (著名写手)
刘苏州
- 模拟EPI: 8
- 应助: 9 (幼儿园)
- 贵宾: 4.85
- 金币: 2332.8
- 红花: 1
- 帖子: 1344
- 在线: 271小时
- 虫号: 592012
- 注册: 2008-09-03
- 专业: 理论和计算化学
- 管辖: 分子模拟
★ ★ ★ ★
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
|
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