PyMOL绘制的多肽配体经过AutoDock Vina分子对接后，C端双键总是消失该如何解决

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各位老师好，我的配体是用PyMOL绘制的多肽，受体是蛋白质。在对接前我使用PyMOL的Builder功能对多肽的N端和C端进行了修饰，如下图。但是在经过AutoDock Vina分子对接后，配体C端的这个双键变成了单键，如下图，这让我百思不得其解，不知道有没有别人也遇到过这种情况，感谢各位老师的回复。

SiqiLee

要不尝试一下加个帽子试试？Cap，两端分别加上ACE和NME试试呢？

student0618

In theory the two oxygens are equivalent.

In pymol its just a kind of display issue, you may check the difference in atom type etc.

BTW vina is not good for peptide docking due to its limits in modelling the peptide bond. For peptides with standard amino acids there are other software for that, like lightdock, haddock, cabsdock etc. I skip alphafold3 server due to the highly restricted terms of usage, but in theory it can also be used.

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SiqiLee 发表于 2024-8-30 08:22
要不尝试一下加个帽子试试？Cap，两端分别加上ACE和NME试试呢？

不好意思，我不太明白Cap是什么意思，加帽子是在PyMOL里进行吗

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student0618 发表于 2024-8-30 10:13
In theory the two oxygens are equivalent.

In pymol its just a kind of display issue, you may chec ...

Thanks for your answer!