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标题: 求助解决parmed的问题 [打印本页]

作者
Author: lxh 时间: 2022-3-12 15:35
标题: 求助解决parmed的问题
在python下安装的parmed，但是执行时候报错如下：

>>> import parmed as pmd
>>> gmx_top = pmd.load_file('topol.top', xyz='complex.gro')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python3.8/dist-packages/ParmEd-0+unknown-py3.8-linux-x86_64.egg/parmed/formats/registry.py", line 211, in load_file
return cls(filename, *args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/ParmEd-0+unknown-py3.8-linux-x86_64.egg/parmed/gromacs/gromacstop.py", line 353, in __init__
self.coordinates = f.coordinates
  File "/usr/local/lib/python3.8/dist-packages/ParmEd-0+unknown-py3.8-linux-x86_64.egg/parmed/structure.py", line 1696, in coordinates
coords = coords.reshape((-1, len(self.atoms), 3))
ValueError: cannot reshape array of size 23223 into shape (7681,3)

求解，十分感谢！

作者
Author: sobereva 时间: 2022-3-13 07:32
要么拓扑文件有问题，要么拓扑文件和gro对应关系有问题，要么parmED的bug。前两种情况反复检查以避免，最后的情况把这俩文件发给开发者咨询

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