求助使用autodock模拟环肽，发现环肽是刚性的，怎么能创建柔性的环肽？

waka · 发表于 Post on 2025-4-16 17:14:42

用了几种方法得到的环肽都是刚性的，没有办法折叠，是我在能量最小化的时候将他的结构定死了吗？正准备尝试用gromacs构建环肽试试，不清楚是不是autodock的问题。

student0618 · 发表于 Post on 2025-4-16 20:26:52

This link has the related notes on macrocycles, for Vina but likely also applicable to (standard version of) AutoDock
https://autodock-vina.readthedoc ... ing_macrocycle.html

AutoDock Vina is not able to manage directly the flexibility associated with bonds in cyclic molecules. Different approaches can be used to dock macrocyclic molecules, like identifying one or more low energy conformations and docking them as different ligands, but generating them and docking them separately can be a time-consuming task. But AutoDock Vina (and AutoDock-GPU) has a specialized protocol to dock macrocycles while modeling their flexibility on-the-fly.

sobereva · 发表于 Post on 2025-4-17 03:59:30

不要自己在标题里手写【求助】这种标签，http://bbs.keinsci.com/thread-9348-1-1.html里明确说了。这次给你改了，以后注意

sobereva · 发表于 Post on 2025-4-17 16:19:18

注意描述的准确性
gromacs根本没有构建环肽的功能，那叫对环肽进行分子动力学模拟
“几种方法得到的环肽都是刚性的”这种描述也很不确切，只能说对接过程中没有考虑环肽的柔性

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[分子对接] 求助使用autodock模拟环肽，发现环肽是刚性的，怎么能创建柔性的环肽？

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