生成的配位金属复合物无法使用parmed转换

Azrael

  各位老师，我利用Sobtop生成的金属配位复合物无法使用parmed转换，报错如下：

/home/xqx/software/mamba/envs/ztop/lib/python3.12/site-packages/parmed/gromacs/gromacstop.py:1124: GromacsWarning: 58 1-4 pairs were missing from the [ pairs ] section and were set to zero; make sure you know what you're doing!
  warnings.warn('%i 1-4 pairs were missing from the [ pairs ] '
Traceback (most recent call last):
  File "/home/xqx/Documents/sudafangshe/ga/sobtop/ga/parm.py", line 3, in <module>
    gmx_top = pmd.load_file('dotatoc_small_opt.top', xyz='dotatoc_small_opt.gro')
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/xqx/software/mamba/envs/ztop/lib/python3.12/site-packages/parmed/formats/registry.py", line 211, in load_file
    return cls(filename, *args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/xqx/software/mamba/envs/ztop/lib/python3.12/site-packages/parmed/gromacs/gromacstop.py", line 350, in __init__
    f = load_file(xyz, skip_bonds=True)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/xqx/software/mamba/envs/ztop/lib/python3.12/site-packages/parmed/formats/registry.py", line 194, in load_file
    return cls.parse(filename, *args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/xqx/software/mamba/envs/ztop/lib/python3.12/site-packages/parmed/gromacs/gromacsgro.py", line 177, in parse
    leng, ang = box_vectors_to_lengths_and_angles(
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/xqx/software/mamba/envs/ztop/lib/python3.12/site-packages/parmed/geometry.py", line 131, in box_vectors_to_lengths_and_angles
    alpha = acos((b[0]*c[0] + b[1]*c[1] + b[2]*c[2]) / (lb*lc))
                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
ZeroDivisionError: float division by zero



生成流程参考了使用Sobtop超级方便地创建二茂铁的GROMACS的拓扑文件，在Sobtop产生成成键相关(bonded)参数时，选择了指定固定的原子，让GAFF的参数用于描述柔性部分二面角可旋转特征。


可能是parmed不支持sobtop产生函数形式为2的二面角，请问这个问题可以解决吗？

z9527567

用editconf给gro添加下盒子信息就好了。

Azrael

z9527567 发表于 2024-2-1 15:19
用editconf给gro添加下盒子信息就好了。

谢谢老师

wenzihao

Azrael 发表于 2024-3-8 14:59
谢谢老师

您好，请问问题解决了嘛，我碰到了类似的问题，用editconf加了个盒子，但有同样的报错。
1-4 pairs were missing from the [ pairs ] section and were set to zero

Azrael

wenzihao 发表于 2024-5-31 18:09
您好，请问问题解决了嘛，我碰到了类似的问题，用editconf加了个盒子，但有同样的报错。
1-4 pairs were ...

老老实实用MCPB