求助：acpype生成拓扑文件时报错，提示结构间距太大

MOI_001

以下为运行命令：
acpype -i ligand.mol2 -a amber2 -c user -d
报错如下：
[root@192 CXCL8_5d]# acpype -i ligand.mol2 -a amber2 -c user -d
============================================================================
| ACPYPE: AnteChamber PYthon Parser interfacE v. 2023.10.27 (c) 2024 AWSdS |
============================================================================
DEBUG: CLI: -i ligand.mol2 -a amber2 -c user -d
DEBUG: Python Version 3.11.7 | packaged by conda-forge | (main, Dec 23 2023, 14:43:09) [GCC 12.3.0]
DEBUG: Max execution time tolerance is 3h
DEBUG: /home/moi/miniconda3/bin/antechamber -dr no -i ligand.mol2 -fi mol2 -o tmp -fo ac -pf y
DEBUG:
Welcome to antechamber 22.0: molecular input file processor.

Info: The atom type is set to gaff; the options available to the -at flag are
gaff, gaff2, amber, bcc, and sybyl.

Warning: Ignoring Mol2 record type (@<TRIPOS>SET).
Warning: For atom (ID: 41, Name: O6) the best APS is not zero.
Bonds involving this atom are frozen.
Warning: For atom (ID: 42, Name: O7) the best APS is not zero.
Bonds involving this atom are frozen.
Warning: For atom (ID: 43, Name: O8) the best APS is not zero.
Bonds involving this atom are frozen.
Warning: For atom (ID: 44, Name: O9) the best APS is not zero.
Bonds involving this atom are frozen.
Warning: For atom (ID: 45, Name: O10) the best APS is not zero.
Bonds involving this atom are frozen.
Warning: For atom (ID: 46, Name: O11) the best APS is not zero.
Bonds involving this atom are frozen.
Warning: For atom (ID: 47, Name: O12) the best APS is not zero.
Bonds involving this atom are frozen.
Warning: For atom (ID: 48, Name: O13) the best APS is not zero.
Bonds involving this atom are frozen.

ERROR: Atoms TOO scattered (> 3.0 Ang.)
ERROR: ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: ['ATOM 45 O10 ']
['ATOM 46 O11 ']
['ATOM 47 O12 ']
['ATOM 48 O13 ']
ERROR: ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Use '-f' option if you want to proceed anyway. Aborting ...
ERROR: Coordinates issues with your system
ERROR: ACPYPE FAILED: Coordinates issues with your system
Traceback (most recent call last):
  File "/home/moi/miniconda3/lib/python3.11/site-packages/acpype/cli.py", line 106, in init_main
    molecule = ACTopol(
               ^^^^^^^^
  File "/home/moi/miniconda3/lib/python3.11/site-packages/acpype/topol.py", line 3325, in __init__
    self.setResNameCheckCoords()
  File "/home/moi/miniconda3/lib/python3.11/site-packages/acpype/topol.py", line 564, in setResNameCheckCoords
    raise Exception(msg)
Exception: Coordinates issues with your system
Total time of execution: less than a second
DEBUG: No tmp folder left to be removed
Log tmp location: /tmp/tmpmo9ti7fz

实在是不懂结构上出了什么问题，能否请大家看看，谢谢！！
结尾附上mol2文件

sobereva

用sobtop（http://sobereva.com/soft/Sobtop）就没这些破毛病，敲几下键盘拓扑文件就出来了，又省事又方便

MOI_001

sobereva 发表于 2024-1-26 02:14
用sobtop（http://sobereva.com/soft/Sobtop）就没这些破毛病，敲几下键盘拓扑文件就出来了，又省事又方便

请问sob老师，如果我大分子选择的是amber03力场，TIP3P力场，小分子要选择哪个力场呢？

sobereva

MOI_001 发表于 2024-1-26 13:12
请问sob老师，如果我大分子选择的是amber03力场，TIP3P力场，小分子要选择哪个力场呢？

AMBER03完全过时了
如今用AMBER力场描述蛋白质，至少也该用AMBER14SB
有机小分子用GAFF