acpype命令出现错误

黄舒伟 · 发表于 Post on 2021-4-9 10:12:42

请问一下，我按照社长说的http://bbs.keinsci.com/thread-428-1-1.html 用acpype脚本去生成拓扑，用http://svn.code.sf.net/p/ccpn/co ... python/acpype/test/ 中的例子AAA.mol2去复现的时候，出现了报错如下，请问是什么情况呢？（已经chmod 777 ./acpype.py）似乎是引用Antechamber出错了，请问应该怎么解决？（Antechamber在我服务器单独是可以使用的）

(base) [learning@rtx2 2text]$ ./acpype.py -i AAA.mol2
============================================================================
| ACPYPE: AnteChamber PYthon Parser interfacE v. 0 0 Rev: 0 (c) 2021 AWSdS |
============================================================================
WARNING: no 'babel' executable, no PDB file as input can be used!
==> ... charge set to 0
WARNING: Old version of antechamber. Strongly consider upgrading to AmberTools
WARNING: Setting mopac for antechamber
==> Executing Antechamber...
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Welcome to antechamber 19.0: molecular input file processor.
acdoctor mode is on: check and diagnose problems in the input file.
-- Check Format for mol2 File --
Status: pass
Info: Finished reading file (AAA.mol2); atoms read (33), bonds read (32).
-- Check Unusual Elements --
Status: pass
-- Check Open Valences --
Status: pass
-- Check Geometry --
for those bonded
for those not bonded
Status: pass
-- Check Weird Bonds --
Status: pass
-- Check Number of Units --
Status: pass
acdoctor mode has completed checking the input file.
Running: /home/alvin/apps/anaconda3/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
---Judge bond type for Residue 1 with ID of 1 and Name of ALA ---
---Judge bond type for Residue 2 with ID of 2 and Name of ALA ---
---Judge bond type for Residue 3 with ID of 3 and Name of ALA ---
Running: /home/alvin/apps/anaconda3/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Info: Total number of electrons: 124; net charge: 0
Running: /home/alvin/apps/anaconda3/bin/mopac.sh
sh: /home/alvin/apps/anaconda3/bin/mopac.sh: No such file or directory
/home/alvin/apps/anaconda3/bin/to_be_dispatched/antechamber: Fatal Error!
Cannot properly run "/home/alvin/apps/anaconda3/bin/mopac.sh".
++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Antechamber failed
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Cannot open file (AAA_bcc_gaff.mol2) with mode (r).
No such file or directory
++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Parmchk failed
ERROR: Tleap failed
==> Removing temporary files...
ACPYPE FAILED: [Errno 2] No such file or directory: 'AAA_AC.prmtop'
Total time of execution: less than a second

复制代码

黄舒伟 · 发表于 Post on 2021-4-23 11:22:16

黄舒伟发表于 2021-4-10 16:54
社长，我想请问一下，我按您说的更改了文件参数后，可以正确生成AAA.mol2的拓扑，但是对于我想要生成的H.mo ...

查阅了前人的经验，应该是ambertools的版本有问题，不过也没去安装最新的去试，比较在线的就可以的话那本地是否可以也就无所谓了。

黄舒伟 · 发表于 Post on 2021-4-10 16:54:37

本帖最后由黄舒伟于 2021-4-11 13:19 编辑

社长，我想请问一下，我按您说的更改了文件参数后，可以正确生成AAA.mol2的拓扑，但是对于我想要生成的H.mol2的拓扑却出现了如下报错（在您说的在线的acpype网站上能正确H.mol2的拓扑）：

(base) [learning@rtx2 text]$ ./acpype.py -i H.mol2 -c user
============================================================================
| ACPYPE: AnteChamber PYthon Parser interfacE v. 0 0 Rev: 0 (c) 2021 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

复制代码

想请问一下为什么会出现这种情况呢？

黄舒伟 · 发表于 Post on 2021-4-10 10:01:02

社长，永远的神！

sobereva · 发表于 Post on 2021-4-10 01:32:15

看上去是调用MOPAC出错
要求acpype不做几何优化再试

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