用途
为Amber分子动力学模拟准备所需的拓扑和坐标文件。支持生物大分子、有机小分子体系,暂不支持膜蛋白。
预备知识
溶剂模型
通常研究的有机生物体系是在溶液(尤其是水溶液)中进行的,水对蛋白折叠、热力学性质有着极为重要的影响。为了反映溶剂化效应,一般要在分子动力学模拟中采用溶剂模型。溶剂模型可分为两类:显式溶剂模型(explicit solvent model)和隐式溶剂模型(implicit solvent model)。
- 显式溶剂模型
该模型直接将研究体系放在水盒子中,通常还添加抗衡离子以中和体系电荷。这种直接模拟溶质与溶剂之间相互作用的方法,大大提高了模拟的准确性,但大量水分子也会带来计算量的急剧增加。通常使用一定大小的水盒子把溶质包裹起来,采用周期边界条件(periodic boundary condition,PBC)来表现无限溶剂环境。
- 隐式溶剂模型
该模型不添加水分子,而用连续介质模型(数学方程)来反映该效应。隐式溶剂模型有许多优势,包括:减少体系粒子数目,降低计算开销;无溶剂摩擦效应,加快构像变化,避免长时间模拟;无需显式水的平衡过程。最著名的模型为广义波恩(Generalized Born,GB)方法。
通常,我们在做常规分子动力学模拟时会采用显式溶剂模型,而在之后的结合自由能计算则采用隐式溶剂模型(MM/GB(PB)SA方法)。
水模型
显式溶剂模型需要在溶质周围填充水分子,至今已经发展出许多水模型,以重现水的不同性质。Amber中可使用的水模型包括:TIP3P、TIP3P/F、TIP4P、TIP4P/Ew、TIP5P、OPC、OPC、POL3、SPC/E、SPC/Eb、TIP3PFB和TIP4PFB。此外,还有有机溶剂非可极化模型,包括:甲醇、氯仿、N-甲基乙酰胺以及尿素-水混合溶剂。
其中,最常用的水模型是TIP3P。该模型已经被证实在许多性质上与真实水存在不少差距。但由于历史原因,过去很多力场都是基于TIP3P水模型建立的,总能量中溶剂部分的误差在一定程度上被抵消了。TIP3P水模至今仍然在生物分子模拟中非常流行。
OPC是一个新的非极化、4点、3电荷刚性水模型,它在许多性质上显著更好于常用的刚性水模型(如TIP3P)。最近对AMBER ff99SB的更新,消除了它对TIP3P水模型固有的偏倚,OPC也因此成为与之搭配使用的首推之选。
更多关于水模型的介绍,请见Amber 20手册第52-54页。
入口
平台地址:https://cloud.yinfotek.com/
功能入口:左侧菜单栏【计算方案】->【小工具】->【分子动力学】->【准备Amber文件】
步骤
1. 上传分子结构
上传处理好的3D分子结构文件。分子无残基、氢原子缺失,mol2文件还需带有原子电荷(请参照【处理PDB结构(进阶版)】、【准备化合物结构】和【添加原子电荷】等教程)。
- 强烈建议:生物大分子(蛋白、核酸、多糖、磷脂)、辅酶、水、金属离子等结构采用pdb格式文件,有机小分子用mol2格式。
- 相同格式的组分,可合并为一个文件,也可分别上传。如下图,receptor.pdb包含蛋白、核酸、多糖、磷脂、辅酶、水和金属离子,ligand-A.mol2和ligand-B.mol2为有机小分子。
- 上传多个mol2文件时需要注意顺序,因为这决定了它们在研究体系中的排列顺序。例如,先上传ligand-A.mol2后上传ligand-B.mol2,那么,在复合物体系中,它们的顺序是AB;反之为BA。
当有mol2文件时,会自动显示其残基名,用户可修改为合适的名称,以便准确标记该分子,方便后续分析。残基名由三个(通常大写)英文字母和(或)阿拉伯数字组成,例如:BAX。
如下图所示,ligand-A.mol2文件包含2个分子,残基分别为BAX和BAY,而ligand-B.mol2文件包含1个分子,残基名为YF5。
2. 上传参数文件
参数文件不是必须的,通常用于补充缺失的、特殊的参数,如:修饰后残基(非标准残基)的参数文件、辅酶参数文件、【添加原子电荷】时提示缺少的某些参数、特殊处理的金属参数。
3. 设置模拟环境
有机生物体系通常在溶剂环境中进行模拟。若需使用显式溶剂,可通过该设置添加溶剂和离子。
4. 分子力场
默认采用以下Amber力场,且目前暂不支持变更:
- ff19SB:蛋白
- BSC1:DNA
- OL3:RNA
- GLYCAM_06j:多糖
- lipid17:磷脂
-
GAFF2:有机小分子(支持C、N、O、S、P、H、F、Cl、Br和I等元素)
5. 查看体系,下载文件 amber_files.zip
。
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