计算rmsd分为2种，一种是直接计算，另一种是先叠合再计算。

强烈推荐使用schrodinger中superposition。

不推荐使用pymol的align以及rms以及rms_cur计算。

参考

http://www.schrodinger.com/kb/1532

                    Can I superimpose conformers based on a subset of the atoms in the structure, like all heavy atoms, or the atoms in a particular ring?                

                  Yes. This feature is available in the Superposition panel in Maestro. To superimpose a set of conformers using a SMARTS pattern for the atoms, do the following:

1. In the Project Table, select all of the conformers, and include just one in the Workspace (by clicking the In box for the first structure row).

2. Choose Tools → Superposition.

3. Under "Entries to superimpose" select "Selected entries". If you want to create a property from the RMSD value, select "Create RMSD Property"

这里我的构象都已经叠合过了，所以我勾选了 in place 选项，直接计算RMSD就可以了。

If you want to superimpose the conformers by "all heavy atoms", then instead of using the SMARTS tab, use the ASL tab, enter "not a.e H" in the"Superimpose by ASL" text box, and press Enter key.

To see the results, go to the Project Table and include the first conformer. Then scroll the table to the final conformer, and shift-click the "In" box for the final structure to display all of the structures in the Workspace.                                    

Keywords:                    Maestro, superpose  

蛋白rmsd计算的时候，强烈建议排除H原子，因为H原子是后来加上去的，不确定性太强。

#rmsd的计算log文件的解读

删除所有比较蛋白中的H原子

#Mols: 1 - 46; RMS =   9.5841; Maximum Diff =  33.1914 between atoms  1140 &  1140

蛋白的“1-46”和参照蛋白的RMS为9.5841，其中原子对应的rmsd最大的值为33.1914，参照蛋白有1140个原子，“1-46”有1140个原子

只删除参照蛋白中的H原子

#Mols: 1 - 46; RMS =   9.5841; Maximum Diff =  33.1914 between atoms  1140 &  2309

蛋白的“1-46”和参照蛋白的RMS为9.5841，其中原子对应的rmsd最大的值为33.1914，参照蛋白有1140个原子，“1-46”有2309个原子

#rmsd的计算结果

           

 

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