标题: 采用acpype.py生成离子液体阳离子拓扑文件报错 [打印本页] 作者Author: 陈小黑啊啊啊 时间: 2022-10-31 09:36 标题: 采用acpype.py生成离子液体阳离子拓扑文件报错 请问采用acpype.py文件生成离子液体阳离子报错。报错如下，请问是什么情况？
[root@localhost OHPY]# ./acpype.py -i OHPY.mol2 -n 1
============================================================================
| ACPYPE: AnteChamber PYthon Parser interfacE v. 0 0 Rev: 0 (c) 2022 AWSdS |
============================================================================
WARNING: no 'babel' executable, no PDB file as input can be used!
ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp'
Total time of execution: less than a second
(base) [root@localhost OHPY]# ./acpype.py -i OHPY.mol2 -d
============================================================================
| ACPYPE: AnteChamber PYthon Parser interfacE v. 0 0 Rev: 0 (c) 2022 AWSdS |
============================================================================
DEBUG: Python Version 3.7.3
DEBUG: Max execution time tolerance is 10h
WARNING: no 'babel' executable, no PDB file as input can be used!
DEBUG: /sob/amber18/bin/antechamber -i OHPY.mol2 -fi mol2 -o tmp -fo ac -pf y
DEBUG:
Welcome to antechamber 17.3: molecular input file processor.
acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for mol2 File --
Status: pass
-- Check Unusual Elements --
Status: pass
-- Check Open Valences --
Status: pass
-- Check Geometry --
for those bonded
for those not bonded
Status: pass
-- Check Weird Bonds --
/sob/amber18/bin/to_be_dispatched/antechamber: Fatal Error!
Weird atomic valence (3) for atom (ID: 5, Name: C5).
Possible open valence.
ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp'
File "./acpype.py", line 3558, in <module>
is_sorted=options.sorted, chiral=options.chiral)
File "./acpype.py", line 3155, in __init__
self.setResNameCheckCoords()
File "./acpype.py", line 673, in setResNameCheckCoords
tmpFile = open('tmp', 'r')
Total time of execution: less than a second