student0618 发表于 2024-7-12 18:29
What kind of molecules you are working on? Antechamber is used to handle small molecules, not a whol ...

thank you so much

sobereva 发表于 2024-7-12 18:35
成键方式特殊的情况用antechamber没法转，可以用GaussView、Openbabel转

好的，谢谢sob老师

成键方式特殊的情况用antechamber没法转，可以用GaussView、Openbabel转

如置顶的新社员必读贴、论坛首页的公告栏、版头的红色大字非常明确所示，求助帖必须在帖子标题明确体现出此帖内容是求助或提问，仔细看http://bbs.keinsci.com/thread-9348-1-1.html。我已把你的不恰当标题 “通过antechamber转PDB文件为MOL2文件” 改了，以后务必注意

What kind of molecules you are working on? Antechamber is used to handle small molecules, not a whole protein.
If it is a protein/nucleic acid with standard forcefield parameters available, you should use the forcefield files provided and prepare the file in tleap/xleap. Refer to amber tutorials on their official website for details.