MMPBSA.py.MPI计算小分子抑制剂和人体BET蛋白的结合自由能时报错

studying · 发表于 Post on 2024-5-7 18:06:32

老师，我在使用MMPBSA.py.MPI计算小分子抑制剂和人体BET蛋白的结合自由能时，由于小分子内含有氟原子，所以出现了以下报错：
应该怎么办呢

rpestana94 · 发表于 Post on 2024-5-7 22:21:32

The fluorine by itself shouldn't be the problem, you already run a molecular dynamics simulation, so I assumed that the parameters file are ok, Did you try to run without using mpi?

sobereva · 发表于 Post on 2024-5-8 06:04:49

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，并清楚、准确反映出帖子具体内容，避免有任何歧义和含糊性，仔细看http://bbs.keinsci.com/thread-9348-1-1.html。我已把你的不恰当标题 “MMPBSA，分子动力学” 改了，以后务必注意！下次将删帖+扣分处理。

Huschein · 发表于 Post on 2024-5-8 15:03:18

amber用户建议直接用sander，gmx用户建议gmx MMPBSA

studying · 发表于 Post on 2024-5-9 14:02:11

rpestana94 发表于 2024-5-7 22:21
The fluorine by itself shouldn't be the problem, you already run a molecular dynamics simulation, so ...

Thank you for your answer. I tried not to use MPI, but I still reported the following errors：
[proxy:0:0@localhost.localdomain] HYDU_create_process (../../utils/launch/launch.c:588): execvp error on file /home/chenlin/soft/software/amber12/bin/MMPBSA (No such file or directory)
[proxy:0:0@localhost.localdomain] HYDU_create_process (../../utils/launch/launch.c:588): execvp error on file /home/chenlin/soft/software/amber12/bin/MMPBSA (No such file or directory)
[proxy:0:0@localhost.localdomain] HYDU_create_process (../../utils/launch/launch.c:588): execvp error on file /home/chenlin/soft/software/amber12/bin/MMPBSA (No such file or directory)
[proxy:0:0@localhost.localdomain] HYDU_create_process (../../utils/launch/launch.c:588): execvp error on file /home/chenlin/soft/software/amber12/bin/MMPBSA (No such file or directory)
[proxy:0:0@localhost.localdomain] HYDU_create_process (../../utils/launch/launch.c:588): execvp error on file /home/chenlin/soft/software/amber12/bin/MMPBSA (No such file or directory)
[proxy:0:0@localhost.localdomain] HYDU_create_process (../../utils/launch/launch.c:588): execvp error on file /home/chenlin/soft/software/amber12/bin/MMPBSA (No such file or directory)
[proxy:0:0@localhost.localdomain] HYDU_create_process (../../utils/launch/launch.c:588): execvp error on file /home/chenlin/soft/software/amber12/bin/MMPBSA (No such file or directory)
[proxy:0:0@localhost.localdomain] HYDU_create_process (../../utils/launch/launch.c:588): execvp error on file /home/chenlin/soft/software/amber12/bin/MMPBSA (No such file or directory)
I hope you can help me. Thank you very much

studying · 发表于 Post on 2024-5-9 14:02:55

sobereva 发表于 2024-5-8 06:04
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 ...

好的，谢谢sob老师，以后我会注意这个问题，给您添麻烦了。

rpestana94 · 发表于 Post on 2024-5-9 22:31:19

studying 发表于 2024-5-9 01:02
Thank you for your answer. I tried not to use MPI, but I still reported the following errors：
H ...

which version of ambertools are you using?

studying · 发表于 Post on 2024-5-10 15:04:14

rpestana94 发表于 2024-5-9 22:31
which version of ambertools are you using?

Dear teacher, I made it with AMBER12.

rpestana94 · 发表于 Post on 2024-5-11 02:59:12

studying 发表于 2024-5-10 02:04
Dear teacher, I made it with AMBER12.

Can you try with a newer version? Is free for non-commercial

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[Amber] MMPBSA.py.MPI计算小分子抑制剂和人体BET蛋白的结合自由能时报错

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