Asking for help in the conformational search of an organic molecule

vitalys · 发表于 Post on 2025-12-28 01:30:47

Hi everyone
I want to perform a conformational search for a flexible organic molecule (attached image). I am familiar with the wonderful tool "Gentor", but I am confused how to correctly handle rotatable bonds in the given molecule, since it has 4 rotatable bonds.
2- Synchronous rotations could be a good choise for this situation ???

Any guidance or suggestions would be greatly appreciated.

mol.xyz (2.2 KB, 下载次数 Times of downloads: 0)

sobereva · 发表于 Post on 2025-12-28 07:10:13

You should use gentor (a component of molclus) to independently rotate the four bonds. Assume that rotating each bond by three times, then totally you will generate 3^4=81 initial conformers.

vitalys · 发表于 Post on 2025-12-28 22:56:50

sobereva 发表于 2025-12-28 07:10
You should use gentor (a component of molclus) to independently rotate the four bonds. Assume that r ...

Thank you very much for your answer. Could you give me your opinion about chosen angles values for Gentor:

sobereva · 发表于 Post on 2025-12-30 14:45:19

vitalys 发表于 2025-12-28 22:56
Thank you very much for your answer. Could you give me your opinion about chosen angles values for ...

Rotating B4 by 180 degree is meaningless, because this results in exactly the same structure. Its stepsize should also be set to 120.

		自动登录 Automatic login	找回密码 Forget password
密码 Password			注册 Register

[Molclus] Asking for help in the conformational search of an organic molecule

浏览过的版块