Sobtop结合ParmEd产生Amber拓扑文件报错

Kalinite

请问各位老师：我想使用Sobtop产生GROMACS格式的拓扑文件，然后再用ParmEd转换成Amber格式的拓扑文件。在操作时出现了以下有关1-4项的问题，但是Sobtop产生的GROMACS拓扑文件中显示不需要定义1-4项。涉及的相关文件在附件压缩包中。

1. /home/miniconda3/envs/AmberTools22/lib/python3.10/site-packages/parmed/gromacs/gromacstop.py:1022: GromacsWarning: 25 1-4 pairs were missing from the [ pairs ] section and were set to zero; make sure you know what you're doing!
   
2.   warnings.warn('%i 1-4 pairs were missing from the [ pairs ] '
   
3. Traceback (most recent call last):
   
4.   File "/home/xjw/fe2og/prepare-akg/top/akg.py", line 4, in <module>
   
5.     gmx_top = pmd.load_file('akg.itp', xyz='akg.gro')
   
6.   File "/home/miniconda3/envs/AmberTools22/lib/python3.10/site-packages/parmed/formats/registry.py", line 213, in load_file
   
7.     return cls(filename, *args, **kwargs)
   
8.   File "/home/miniconda3/envs/AmberTools22/lib/python3.10/site-packages/parmed/gromacs/gromacstop.py", line 255, in __init__
   
9.     f = load_file(xyz, skip_bonds=True)
   
10.   File "/home/miniconda3/envs/AmberTools22/lib/python3.10/site-packages/parmed/formats/registry.py", line 196, in load_file
    
11.     return cls.parse(filename, *args, **kwargs)
    
12.   File "/home/miniconda3/envs/AmberTools22/lib/python3.10/site-packages/parmed/gromacs/gromacsgro.py", line 188, in parse
    
13.     leng, ang = box_vectors_to_lengths_and_angles(
    
14.   File "/home/miniconda3/envs/AmberTools22/lib/python3.10/site-packages/parmed/geometry.py", line 131, in box_vectors_to_lengths_and_angles
    
15.     alpha = acos((b[0]*c[0] + b[1]*c[1] + b[2]*c[2]) / (lb*lc))
    
16. ZeroDivisionError: float division by zero

复制代码

akg.rar (431.37 KB, 下载次数 Times of downloads: 0)

2022-8-29 21:04 上传 Uploaded

点击下载
Click to download