嗯 搞一下

心向暖阳 发表于 2022-1-7 09:37
ztop
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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~

ztop
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acpype没法直接产生带过渡金属的小分子的拓扑文件

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

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