求助：为什么acpype.py生成小分子的top文件时，linux系统会报错？

FLO

体系：采用amber+GAFF力场分子对BSA牛血清蛋白和类黄酮-金属离子配合物小分子的动力学模拟。小分子结构采用GaussView 6.0优化，用acpype.py产生小分子配合物的top文件时，系统报错，无法进行下一步模拟。麻烦大家帮我看一下，到底是哪里出了问题呢？要如何修正呢？超级感谢！
1. 首先antechamber 17.3 是运行正常的

2. 调用acpype.py计算时，出现如下界面：

3. 尝试调用acpype_noopt.py计算，仍然出现相同语句：

4. 小分子配合物CU.mol2文件：


5. 小分子配合物CU.pdb文件：

snljty

加上-d参数输出debug信息看看再说。
这文件直接贴图，别人要想测试还得一行一行敲进去。建议直接把文件（压缩后）做附件贴上来

FLO

snljty 发表于 2022-1-6 19:59
加上-d参数输出debug信息看看再说。
这文件直接贴图，别人要想测试还得一行一行敲进去。建议直接把文件（ ...

谢谢，命令里加上-d 了，附件已上传。看了下面的说明，我还是有几个问题：1. python 版本有问题？2. Max execution time tolerance is 10h 这个我不清楚是什么意思 3.  Unusual Elements里的Cu参数是直接用高斯优化后的，现在报错的意思是需要我在GAFF力场里复制Cu的参数手动修改吗？4. “tmp“这个问题我不知道怎么解决。
[root@localhost BSA-1]# ./acpype.py -i CU.mol2 -n 0 -d
============================================================================
| ACPYPE: AnteChamber PYthon Parser interfacE v. 0 0 Rev: 0 (c) 2022 AWSdS |
============================================================================
DEBUG: Python Version 2.7.5
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 CU.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 --
Warning: Unusual element (Cu) for atom (ID: 29, Name: Cu29).
GAFF does not have sufficient parameters for molecules having unusual
         elements (those other than H,C,N,O,S,P and halogens).
         To ensure antechamber works properly, one may need to designate
         bond types for bonds involved with unusual elements.
         To do so, simply freeze the bond types by appending "F" or "f"
         to the corresponding bond types in ac or mol2 files.
-- Check Open Valences --
Warning: The number of bonds (2) for atom (ID: 2, Name: O2) does not match
         the connectivity (1) for atom type (O) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (2) for atom (ID: 3, Name: C3) does not match
         the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (2) for atom (ID: 23, Name: O23) does not match
         the connectivity (1) for atom type (O) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (2) for atom (ID: 24, Name: O24) does not match
         the connectivity (1) for atom type (O) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (2) for atom (ID: 25, Name: O25) does not match
         the connectivity (1) for atom type (O) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (2) for atom (ID: 27, Name: O27) does not match
         the connectivity (1) for atom type (O) defined in CORR_NAME_TYPE.DAT.
But, you may safely ignore the warnings if your molecule
         uses atom names or element names as atom types.
-- 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: 3, Name: C3).
       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

sobereva

acpype没法直接产生带过渡金属的小分子的拓扑文件

心向暖阳

ztop
go

FLO

心向暖阳 发表于 2022-1-7 09:37
ztop
go

您好，我刚在论坛上查了ztop，您是建议我用“[程序/脚本开发] 构建及优化[小大]分子力场参数脚本ztop.py”这个脚本试一下嘛？谢谢回复~

心向暖阳

嗯 搞一下