计算化学公社

标题: mmpbsa.py计算结合自由能时报错问题寻求解答 [打印本页]

作者
Author: Dongxiao 时间: 2022-8-9 09:35
标题: mmpbsa.py计算结合自由能时报错问题寻求解答
我在用mmpbsa.py计算蛋白和小分子的结合自由能时，gb算完之后，pb报错了，报错信息如下：
File "/share/home/user/apps/amber/amber20/lib/python3.9/site-packages/MMPBSA_mods/calculation.py", line 428, in run
error_list = [s.strip() for s in out.split('\n')
TypeError: a bytes-like object is required, not 'str'

Fatal Error!
All files have been retained for your error investigation:
You should begin by examining the output files of the first failed calculation.
Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
manual for file naming conventions.
我的gb部分已经算完了，所以我觉得我的三个prmtop文件应该没有问题，我实在不知道问题出在哪里导致计算报错，
我自己尝试了很多方法，都没有解决我的问题，看了以前的论坛帖子，大家也都没有遇到类似的问题，有没有哪位老师能够帮我解答一下，谢谢

作者
Author: rpestana94 时间: 2022-8-9 21:17
Quite strange behaviour considering that gb calculation run without any kind of problem, maybe you can try generating the files again or re install

作者
Author: Dongxiao 时间: 2022-8-11 12:06

rpestana94 发表于 2022-8-9 21:17
Quite strange behaviour considering that gb calculation run without any kind of problem, maybe you c ...

I found the solution to this problem, because I have Fe atom in my protein, therefore I need to use radiopt=0 pb calculation parameter in my input file.

作者
Author: rpestana94 时间: 2022-8-11 21:59

Dongxiao 发表于 2022-8-10 23:06
I found the solution to this problem, because I have Fe atom in my protein, therefore I need to us ...

Nice, I will have that in mind if I ever had that problem

欢迎光临计算化学公社 (http://bbs.keinsci.com/)