标题: CGenFF创建小分子拓扑文件报错 [打印本页] 作者Author: LvYang 时间: 2022-10-11 23:40 标题: CGenFF创建小分子拓扑文件报错 我在使用gromacs学习蛋白与配体的分子动力学模拟时，在创建小分子的拓扑文件时遇到报错指令，具体报错问题如下：
(py_gmx) C:\Users\HP\Desktop\gmx_test2>python cgenff_charmm2gmx_py3_nx2.py jz4 jz4.mol2 jz4.str charmm36.ff
NOTE 1: Code tested with Python 3.5.2 and 3.7.3. Your version: 3.5.6 |Anaconda, Inc.| (default, Aug 26 2018, 16:05:27) [MSC v.1900 64 bit (AMD64)]
NOTE 2: Code tested with NetworkX 2.3. Your version: 2.3
NOTE 3: Please be sure to use the same version of CGenFF in your simulations that was used during parameter generation:
--Version of CGenFF detected in jz4.str : 4.6
--Version of CGenFF detected in charmm36.ff/forcefield.doc : 4.6
NOTE 4: To avoid duplicated parameters, do NOT select the 'Include parameters that are already in CGenFF' option when uploading a molecule into CGenFF.
Error in atomgroup.py: read_mol2_coor_only: no. of atoms in mol2 (22) and top (0) are unequal
Usually this means the specified residue name does not match between str and mol2 files
报错说mol2与str文件中的残疾名不匹配，但是我检查后发现文件中的残基名是对应的上的，如下：
我十分困惑不解，各位老师能抽出时间解答我的疑惑吗，十分感谢！！！