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标题: 使用网站acpype生成拓扑文件出现以下错误 [打印本页]

作者
Author: mnmn 时间: 2024-5-23 13:00
标题: 使用网站acpype生成拓扑文件出现以下错误
网站：https://www.bio2byte.be/acpype/

生成拓扑文件时出现错误不知道如何解决，希望有大佬指教！

Logs for bQ3vRfx56lYRyGcIskHq | n20.pdb | Sat May 04 14:15 2024Details

Hash ID: bQ3vRfx56lYRyGcIskHq
Submission date: May 4, 2024, 2:15 p.m.
Submission filename: n20.pdb
Job status: Failed
Input type: INPUT_FILE
Smiles?: None
Charge type: bcc
Net charge: auto
Multiplicity: 1
Atom type: gaff

Log file===========================================================================| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.7.21 (c) 2024 AWSdS |===========================================================================DEBUG: Python Version 3.7.7 (default, Mar 10 2020, 15:16:38) [GCC 7.5.0]DEBUG: Max execution time tolerance is 1hDEBUG: /home/b2b-user/web/lib/python3.7/site-packages/acpype/amber21-11_linux/bin/antechamber -dr no -i n20.pdb.mol2 -fi mol2 -o tmp -fo ac -pf yDEBUG: Welcome to antechamber 21.0: molecular input file processor.The atom type is set to gaff; the options available to the -at flag are gaff, gaff2, amber, bcc, and sybyl.Info: Bond types are assigned for valence state (2) with penalty (1).DEBUG: setResNameCheckCoords doneWARNING: no charge value given, trying to guess one...DEBUG: /home/b2b-user/web/lib/python3.7/site-packages/acpype/amber21-11_linux/bin/antechamber -dr no -i n20.pdb.mol2 -fi mol2 -o tmp -fo mol2 -c gas -pf nDEBUG: /home/b2b-user/web/lib/python3.7/site-packages/acpype/amber21-11_linux/bin/antechamber -dr no -i tmp -fi mol2 -o tmp -fo mol2 -c wc -cf tmp.crg -pf nDEBUG: ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++DEBUG: Welcome to antechamber 21.0: molecular input file processor.The atom type is set to gaff; the options available to the -at flag are gaff, gaff2, amber, bcc, and sybyl.Info: Bond types are assigned for valence state (2) with penalty (1).DEBUG: ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++DEBUG: readMol2TotalCharge: -1.0DEBUG: Net charge drift '0.000000'==> ... charge set to -1==> Executing Antechamber...DEBUG: /home/b2b-user/web/lib/python3.7/site-packages/acpype/amber21-11_linux/bin/antechamber -dr no -i n20.pdb.mol2 -fi mol2 -o n20.pdb.mol2_bcc_gaff.mol2 -fo mol2 -c bcc -nc -1 -m 1 -s 2 -df 2 -at gaff -pf n DEBUG: No file left to be removedERROR: ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ERROR: Welcome to antechamber 21.0: molecular input file processor.The atom type is set to gaff; the options available to the -at flag are gaff, gaff2, amber, bcc, and sybyl.Info: Finished reading file (n20.pdb.mol2); atoms read (31), bonds read (32).Info: Determining atomic numbers from atomic symbols which are case sensitive.Running: /home/b2b-user/web/lib/python3.7/site-packages/acpype/amber21-11_linux/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f acInfo: Bond types are assigned for valence state (2) with penalty (1).Running: /home/b2b-user/web/lib/python3.7/site-packages/acpype/amber21-11_linux/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaffInfo: Total number of electrons: 171; net charge: -1Info: The number of electrons is odd (171). Please check the total charge (-nc flag) and spin multiplicity (-m flag).Running: /home/b2b-user/web/lib/python3.7/site-packages/acpype/amber21-11_linux/bin/sqm -O -i sqm.in -o sqm.out/home/b2b-user/web/lib/python3.7/site-packages/acpype/amber21-11_linux/bin/wrapped_progs/antechamber: Fatal Error!Cannot properly run "/home/b2b-user/web/lib/python3.7/site-packages/acpype/amber21-11_linux/bin/sqm -O -i sqm.in -o sqm.out".ERROR: ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ERROR: Antechamber failedDEBUG: /home/b2b-user/web/lib/python3.7/site-packages/acpype/amber21-11_linux/bin/parmchk2 -i n20.pdb.mol2_bcc_gaff.mol2 -f mol2 -o n20.pdb.mol2_AC.frcmodERROR: ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ERROR: Cannot open file (n20.pdb.mol2_bcc_gaff.mol2) with mode (r).No such file or directoryERROR: ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ERROR: Parmchk failedERROR: Tleap failedACPYPE FAILED: [Errno 2] No such file or directory: 'n20.pdb.mol2_AC.prmtop' File "/home/b2b-user/web/lib/python3.7/site-packages/acpype/acs_api.py", line 129, in acpype_api molecule.createMolTopol() File "/home/b2b-user/web/lib/python3.7/site-packages/acpype/topol.py", line 1116, in createMolTopol self.topFileData = open(self.acTopFileName).readlines()Total time of execution: less than a secondServer messages

Waiting for initializing the ACPYPE process. [Attempt 1/2] Error ACPYPE: ERROR: [Errno 2] No such file or directory: 'n20.pdb.mol2_AC.prmtop'. [Attempt 2/2] Error ACPYPE: ERROR: [Errno 2] No such file or directory: 'n20.pdb.mol2_AC.prmtop'.

作者
Author: sobereva 时间: 2024-5-23 15:06
用sobtop就完了，省事简单快速，还没那么多破毛病。acpype完全可以弃了
http://sobereva.com/soft/Sobtop

作者
Author: mnmn 时间: 2024-5-23 16:51

sobereva 发表于 2024-5-23 15:06
用sobtop就完了，省事简单快速，还没那么多破毛病。acpype完全可以弃了
http://sobereva.com/soft/Sobtop

感谢你的回答！我下载了sobtop，并依据官网步骤进行操作，想要生成GAFF力场的小分子拓扑文件。在运行中显示操作完成，但拓扑文件我却不知道在哪里获得，我是在压缩包的examples文件夹内新建一个文件夹放置我的小分子，但在相应文件夹并没有发现应生成的拓扑文件，请问我是在操作上有什么错误吗？求指正！

作者
Author: sobereva 时间: 2024-5-24 04:33

mnmn 发表于 2024-5-23 16:51
感谢你的回答！我下载了sobtop，并依据官网步骤进行操作，想要生成GAFF力场的小分子拓扑文件。在运行中显 ...

就在当前目录下产生
搞清楚什么叫当前目录，这是计算机最基本常识。linux下运行pwd命令显示的目录，以及windows下双击运行sobtop.exe时sobtop.exe所在的目录

作者
Author: mnmn 时间: 2024-5-24 18:28
本帖最后由 mnmn 于 2024-5-24 18:31 编辑

sobereva 发表于 2024-5-24 04:33
就在当前目录下产生
搞清楚什么叫当前目录，这是计算机最基本常识。linux下运行pwd命令显示的目录，以及 ...

找到了，感谢

作者
Author: mnmn 时间: 2024-5-24 18:33

sobereva 发表于 2024-5-24 04:33
就在当前目录下产生
搞清楚什么叫当前目录，这是计算机最基本常识。linux下运行pwd命令显示的目录，以及 ...

另外，我话有一个疑问。
3 Assign GAFF atom types as much as possible
当我选择以上GAFF力场，后出现的以下选项：
Well, LJ parameters of all atoms can be found in LJ_param.dat. Now we go to next stage

How to generate bonded parameters for the topology file?
Note: "prebuilt" parameters in this context refer to those in bonded_param.dat
0 Return
1 Without bonded parameters
2 All bonded parameters are determined by mSeminario method
3 Prebuilt bonded parameters if possible, missing ones are supplemented by mSeminario method
4 Same as option 3, but missing ones are arbitrarily guessed
5 Bonded parameters related to selected atoms (usually rigid region) are determined by mSeminario method, others use prebuilt bonded parameters, then missing ones are supplemented by mSeminario method
6 Same as option 5, but missing ones are arbitrarily guessed
7 All bond and angle parameters are determined by mSeminario method, others use prebuilt bonded parameters, then missing ones are supplemented by mSeminario method

我应该如何选择？

作者
Author: sobereva 时间: 2024-5-25 04:09

mnmn 发表于 2024-5-24 18:33
另外，我话有一个疑问。
3 Assign GAFF atom types as much as possible
当我选择以上GAFF力场，后出现 ...

把sobtop主页http://sobereva.com/soft/Sobtop完整看了自然就明白了，例子给得清楚得没法更清楚、用法解释得没法更明白

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