mmpbsa的计算问题

lily49

1，在用mmpbsa.py计算时，总是报错length mismatch in energy vectors
File "/opt/apps/amber16/bin/MMPBSA.py", line 108, in <module>
    app.parse_output_files()
  File "/opt/apps/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 944, in parse_output_files
    self.INPUT['verbose'], self.using_chamber)
  File "/opt/apps/amber16/lib/python2.7/site-packages/MMPBSA_mods/amber_outputs.py", line 1007, in __init__
    self.delta2()
  File "/opt/apps/amber16/lib/python2.7/site-packages/MMPBSA_mods/amber_outputs.py", line 1234, in delta2
    self.com.fill_composite_terms()
  File "/opt/apps/amber16/lib/python2.7/site-packages/MMPBSA_mods/amber_outputs.py", line 372, in fill_composite_terms
    self.data[component] = self.data[key] + self.data[component]
  File "/opt/apps/amber16/lib/python2.7/site-packages/MMPBSA_mods/amber_outputs.py", line 61, in __add__
    raise LengthError('length mismatch in energy vectors')
LengthError: length mismatch in energy vectors

不知道是为什么……
2，改用pbsa.pl计算，由于拓扑体系中加入了使体系维持电中性的Na离子，不知道该怎么在脚本中处理这个Na离子，导致生成的坐标文件和复合物拓扑的原子数不一致了
请问该怎么处理呢？？

rpestana94

mmpbsa in Amber by default strip ions atoms which give you the inconsistent, so you need to specify which atoms do you want to strip, add strip_mask keyword in the input file to do this, look it in the amber manual. Although I don't know if that will solve the problem, when is an atom mismatch with strip_mask you can solve it this is a different error but you can try.

We usually strip Na atoms from the system, if the Na atoms are part of the protein as cofactors or something like that you keep it but if just are added to make the system neutral we strip it.  

lilylotus

rpestana94 发表于 2021-3-31 20:07
mmpbsa in Amber by default strip ions atoms which give you the inconsistent, so you need to specify  ...

thank u so much! I'll try!!!

lilylotus

rpestana94 发表于 2021-3-31 20:07
mmpbsa in Amber by default strip ions atoms which give you the inconsistent, so you need to specify  ...

It worked! Thank you!!!!

rpestana94

lilylotus 发表于 2021-4-2 07:39
It worked! Thank you!!!!

Glad to hear it work, I had the same problem a time ago, it took me about one week to find the solution, so glad to help you to solve this problem