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xingyun5182

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[交流] [求助]Autodock对接结果Reference RMSD过大怎么办？

Autodock对接后的结果显示ref rmsd值很大，都在10左右。
我没有sybyl，因此ligand的pdb文件是用下载的复合物pdb文件中的配体部分用写字板复制粘贴做成的。Ligand和MacroMolecule的相对位置与原复合物pdb中相对位置是相同的。
Autodock的FAQs里说在DPF中可以specify the "rmsref" command，但我在用ADT创建DPF文件的时候并没有找到这个选项，请问这个命令应该如何设定呢？

这是FAQs中的原文：
I get very high Reference RMSD values in my DLG (docking log file); what went wrong?
The "Reference RMSD" values that are printed in the "RMSD TABLE" in the DLG are computed from the coordinates of

either the input ligand (PDBQ or PDBQT) file specified by the "move" command in the DPF, if you did not include the "rmsref" command in your DPF;
or the ligand (PDBQ or PDBQT) file you specified in the "rmsref" command in the DPF.
If you do not specify the "rmsref" command, and the ligand input coordinates happen to be translated far from the receptor, you will appear to get high Reference RMSD values. _Don't Panic!_ This is normal, and you don't need to worry about these high values.

You may want to check that the input ligand coordinates are far from the crystallographically observed binding position in active site, by reading in the input ligand and the receptor in ADT.

We usually use the "rmsref" DPF-command to specify the x-ray crystallographic coordinates of a known binding mode taken from a complex PDB structure. This can be a useful way of checking if your redocking is successful, if the Reference RMSD values are less than 2-3 Å from the crystal structure position of the ligand.

谢谢各位指点。

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