利用./acpype.py -i Lig.mol2 -d 报错信息如下，说找不到amber/bin/mopac.sh

崔智勇

以下报错代码后的内容：如果觉得多可以看图片 ,麻烦老师了
============================================================================
| ACPYPE: AnteChamber PYthon Parser interfacE v. 0 0 Rev: 0 (c) 2021 AWSdS |
============================================================================
DEBUG: Python Version 3.8.8
DEBUG: Max execution time tolerance is 10h
WARNING: no 'babel' executable, no PDB file as input can be used!
DEBUG: /home/cui/.app/amber20/bin/antechamber -i Lig.mol2 -fi mol2 -o tmp -fo ac -pf y
DEBUG:
Welcome to antechamber 21.0: molecular input file processor.

acdoctor mode is on: check and diagnose problems in the input file.
The atom type is set to gaff; the options available to the -at flag are
    gaff, gaff2, amber, bcc, and sybyl.
-- 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   
Warning: Close ( 0.71) nonbonded atoms (ID: 8, Name: N1) and (ID: 36, Name: H11).
Warning: Close ( 1.24) nonbonded atoms (ID: 8, Name: N1) and (ID: 39, Name: H14).
Warning: Close ( 0.88) nonbonded atoms (ID: 12, Name: C7) and (ID: 38, Name: H13).
-- Check Weird Bonds --
   Status: pass
-- Check Number of Units --
   Status: pass
acdoctor mode has completed checking the input file.

Info: Bond types are assigned for valence state (7) with penalty (1).

DEBUG: setResNameCheckCoords done
DEBUG: Net charge drift '0.000000'
==> ... charge set to 0
WARNING: Old version of antechamber. Strongly consider upgrading to AmberTools
WARNING: Setting mopac for antechamber
==> Executing Antechamber...
==> Debugging...
DEBUG: /home/cui/.app/amber20/bin/antechamber -i Lig.mol2 -fi mol2 -o Lig_bcc_gaff.mol2 -fo mol2 -c bcc -nc 0 -m 1 -s 2 -df 0 -at gaff -pf n
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Welcome to antechamber 21.0: molecular input file processor.

acdoctor mode is on: check and diagnose problems in the input file.
The atom type is set to gaff; the options available to the -at flag are
    gaff, gaff2, amber, bcc, and sybyl.
-- Check Format for mol2 File --
   Status: pass
Info: Finished reading file (Lig.mol2); atoms read (45), bonds read (47).
Info: Determining atomic numbers from atomic symbols which are case sensitive.
-- Check Unusual Elements --
   Status: pass
-- Check Open Valences --
   Status: pass
-- Check Geometry --
      for those bonded   
      for those not bonded   
Warning: Close ( 0.71) nonbonded atoms (ID: 8, Name: N1) and (ID: 36, Name: H11).
Warning: Close ( 1.24) nonbonded atoms (ID: 8, Name: N1) and (ID: 39, Name: H14).
Warning: Close ( 0.88) nonbonded atoms (ID: 12, Name: C7) and (ID: 38, Name: H13).
-- Check Weird Bonds --
   Status: pass
-- Check Number of Units --
   Status: pass
acdoctor mode has completed checking the input file.

Running: /home/cui/.app/amber20/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
Info: Bond types are assigned for valence state (7) with penalty (1).

Running: /home/cui/.app/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Info: Total number of electrons: 195; net charge: 0
Info: The number of electrons is odd (195).
      Please check the total charge (-nc flag) and spin multiplicity (-m flag).

Running: /home/cui/.app/amber20/bin/mopac.sh
sh: 1: /home/cui/.app/amber20/bin/mopac.sh: not found
/home/cui/.app/amber20/bin/wrapped_progs/antechamber: Fatal Error!
Cannot properly run "/home/cui/.app/amber20/bin/mopac.sh".

++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Antechamber failed
DEBUG: /home/cui/.app/amber20/bin/parmchk2 -i Lig_bcc_gaff.mol2 -f mol2 -o Lig_AC.frcmod
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Cannot open file (Lig_bcc_gaff.mol2) with mode (r).
No such file or directory
++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Parmchk failed
ERROR: Tleap failed
ACPYPE FAILED: [Errno 2] No such file or directory: 'Lig_AC.prmtop'
  File "./acpype_new.py", line 3510, in <module>
    molecule.createMolTopol()
  File "./acpype_new.py", line 1222, in createMolTopol
    self.topFileData = open(self.acTopFileName, 'r').readlines()
Total time of execution: less than a second

akill

我用21版ambertools也出了这个问题 换18版的ambertools就好了

崔智勇

akill 发表于 2021-7-8 18:33
我用21版ambertools也出了这个问题 换18版的ambertools就好了

请问一下，那老版本的ambertool 你是怎么处理的，可以同时共存两个版本吗？

sobereva

据说把acpype.py脚本里qprog = 'mopac'改成qprog = 'sqm'就可以兼容较新AmberTools，不过我没测试过

崔智勇

sobereva 发表于 2021-7-9 08:29
据说把acpype.py脚本里qprog = 'mopac'改成qprog = 'sqm'就可以兼容较新AmberTools，不过我没测试过

老师您好，全文检索acpype脚本有三处qprog = 'mopac，都改了好像还是不行，不过我把amber20换成amber18就可以了.再次感谢！

Acee

崔智勇 发表于 2021-7-10 09:55
老师您好，全文检索acpype脚本有三处qprog = 'mopac，都改了好像还是不行，不过我把amber20换成amber18就 ...

可以的，我改了就能用了

lyjc19961209

崔智勇 发表于 2021-7-10 09:55
老师您好，全文检索acpype脚本有三处qprog = 'mopac，都改了好像还是不行，不过我把amber20换成amber18就 ...

你好，请问你是怎么改的版本

牧生

lyjc19961209 发表于 2022-2-20 11:11
你好，请问你是怎么改的版本

现在有了更好用，更方便，更快捷，功能更丰富，更傻瓜化的sobtop，无需安装，解压即用，无脑都可以产生高质量的top文件，已经可以彻底放弃acpype了。

http://sobereva.com/soft/Sobtop/

sun877469558

lyjc19961209 发表于 2022-2-20 11:11
你好，请问你是怎么改的版本

我是直接conda新建一个环境，然后装老版本AmberTools18