chatGPT辅助生成molclus懒人脚本：一键完成对复杂天然产物NMR和ECD计算

wlgwhr · 发表于 Post on 2024-2-1 10:36:08

Representative geometry of each cluster along with their energies have been outputted to cluster.xyz in current folder

Temperature for calculating Boltzmann distribution:  350.00 K
# 1 Count: 2 Ratio:  67.68%
# 2 Count: 2 Ratio:  31.96%
# 3 Count: 1 Ratio: 0.27%
# 4 Count: 7 Ratio: 0.06%
# 5 Count: 3 Ratio: 0.02%
mv: cannot stat '04_tem.gjf': No such file or directory
Molclus: A flexible program for searching cluster configurations and molecular conformations
Molclus official website: http://www.keinsci.com/research/molclus.html
Developed by Tian Lu (sobereva@sina.com)    Last update: 2023-Aug-23
Beijing Kein Research Center for Natural Sciences (http://www.keinsci.com)
P-L-E-A-S-E properly cite this code as mentioned in the official site

Inputted trajectory file: 0003_output.xyz
Loading basic information from the inputted trajectory file ...
There are totally       5 geometries in the inputted trajectory file

Setting file: 04_set.ini
Loading setting file ...
Program to be invoked: Gaussian
Task: Frequency
forrtl: No such file or directory
forrtl: severe (29): file not found, unit 12, file /home/ubuntu/molclus112/template.gjf
Image             PC             Routine          Line       Source
molclus          000000000041DBEB  Unknown             Unknown  Unknown
molclus          00000000004383E0  Unknown             Unknown  Unknown
molclus          0000000000412689  Unknown             Unknown  Unknown
molclus          0000000000407A0D  Unknown             Unknown  Unknown
molclus          0000000000404422  Unknown             Unknown  Unknown
libc-2.31.so    000014B8410F5083  __libc_start_main    Unknown  Unknown
molclus          0000000000404329  Unknown             Unknown  Unknown
mv: cannot stat 'template.gjf': No such file or directory
Command of invoking isostat:
./isostat isomers.xyz -Nout 50 -Eout 10.0 -Edis 0.5 -Gdis 0.2 -T 350 -nt 24
Isostat: A statistical analysis tool for a batch of isomers (64 bit)
Released as a component of Molclus, last update of isostat: 2022-May-28
Developed by Tian Lu, contact: sobereva@sina.com
Beijing Kein Research Center for Natural Sciences (http://www.keinsci.com)

Error: Unable to find isomers.xyz
mv: cannot stat 'cluster.xyz': No such file or directory
mv: cannot stat 'isomers.xyz': No such file or directory
ls: cannot access 'gau00*.out': No such file or directory
Molclus: A flexible program for searching cluster configurations and molecular conformations
Molclus official website: http://www.keinsci.com/research/molclus.html
Developed by Tian Lu (sobereva@sina.com)    Last update: 2023-Aug-23
Beijing Kein Research Center for Natural Sciences (http://www.keinsci.com)
P-L-E-A-S-E properly cite this code as mentioned in the official site

Trajectory file 0004_input.xyz cannot be found
版主我看了半天也没看出来哪里的问题，看样子是载入template.gjf文件出了问题，版主可以帮忙看一下如何解决嘛，不胜感激！

欢乐多 · 发表于 Post on 2024-2-2 09:10:26

wlgwhr 发表于 2024-2-1 10:36
Representative geometry of each cluster along with their energies have been outputted to cluster.xyz ...

mv: cannot stat '04_tem.gjf': No such file or directory.
缺少这个文件

herbertsun · 发表于 Post on 2024-2-8 09:49:04

Optimizing all 1 structures of file traj.xyz
forrtl: severe (122): invalid attempt to assign into a pointer that is not associated
Image             PC             Routine          Line       Source
crest             00000000007454D8  crest_restartlog_       399  restartlog.f90
crest             000000000073FC40  crest_restartlog_       86  restartlog.f90
crest             0000000000517B1D  crest_oloop_             213  parallel.f90
crest             00000000004CEBAC  crest_ensemble_op       229  optimization.f90
crest             000000000040425E  MAIN__                   241  crest_main.f90
crest             000000000040334D  Unknown             Unknown  Unknown
crest             00000000026279A0  Unknown             Unknown  Unknown
crest             000000000040322E  Unknown             Unknown  Unknown
Command of invoking isostat:
./isostat crest_ensemble.xyz -Edis 0.5 -Gdis 0.2 -T 350 -nt 24
Isostat: A statistical analysis tool for a batch of isomers (64 bit)
Released as a component of Molclus, last update of isostat: 2022-May-28
Developed by Tian Lu, contact: sobereva@sina.com
Beijing Kein Research Center for Natural Sciences (http://www.keinsci.com)

Error: Unable to find crest_ensemble.xyz
mv: cannot stat 'cluster.xyz': No such file or directory
Molclus: A flexible program for searching cluster configurations and molecular conformations
Molclus official website: http://www.keinsci.com/research/molclus.html
Developed by Tian Lu (sobereva@sina.com)    Last update: 2023-Aug-23
Beijing Kein Research Center for Natural Sciences (http://www.keinsci.com)
P-L-E-A-S-E properly cite this code as mentioned in the official site

Trajectory file as_02_gfn2.xyz cannot be found
Input the path of trajectory file, e.g. /K-ON/Akiyama_MIO.xyz
版主，这个是什么问题呢？

欢乐多 · 发表于 Post on 2024-2-8 10:31:01

herbertsun 发表于 2024-2-8 09:49
Optimizing all 1 structures of file traj.xyz
forrtl: severe (122): invalid attempt to assign into a ...

crest_ensemble.xyz这个文件没有，或者这个文件太大了，结构太多，isostat处理不过来

Jpzzz · 发表于 Post on 2024-4-2 16:18:37

想请问一下楼主如果是超算提交作业（slurm管理系统），是不是可以直接修改10step文件夹里面的.sh文件然后按照顺序提交作业就行

wzkchem5 · 发表于 Post on 2024-4-2 19:31:09

herbertsun 发表于 2024-2-8 02:49
Optimizing all 1 structures of file traj.xyz
forrtl: severe (122): invalid attempt to assign into a ...

报这个错，应该是CREST的bug。正常来说，即使因为用户输入文件写错了，或者文件格式有其他的问题，导致出现这种野指针的问题，程序也有义务在出现野指针问题之前明确告诉用户哪里写错了，并报错退出，无论如何不应该继续执行程序直到真的遇到野指针。
如果你用的CREST不是最新版的话，升级到最新版；如果已经是最新版了，那么建议去CREST的github页面报bug

欢乐多 · 发表于 Post on 2024-4-3 10:00:16

Jpzzz 发表于 2024-4-2 16:18
想请问一下楼主如果是超算提交作业（slurm管理系统），是不是可以直接修改10step文件夹里面的.sh文件然后按 ...

4振动分析、5单点能、NMR和ECD输入文件都是用的3优化的结果输出文件，3的输入文件是2的快速优化的结果，具体你可以试一试吧，molculs不能同时运行这几步，只能一步完成再进行下一步。具体啥情况，可以试一试。

niduhz · 发表于 Post on 2024-5-9 12:35:46

本帖最后由 niduhz 于 2024-5-9 15:11 编辑

Energy and geometry of all successful configurations have been collectively outputted to isomers.xyz in current folder.
In this file, the value after "Frame:" is the frame index in the isomers.xyz, "Step:" is the step number in this time of molclus execution, "Geom:" is geometry index in the inputted trajectory file

grep: 6R_05_sp_orca00*.out: No such file or directory
Shermo: A general code for calculating molecular thermochemistry properties
Version 2.6  Release date: 2024-Feb-11
Developer: Tian Lu (sobereva@sina.com)
Beijing Kein Research Center for Natural Sciences (http://www.keinsci.com)
Official website: http://sobereva.com/soft/shermo

  **** If this code is utilized in your work, PLEASE CITE following paper ****
Tian Lu, Qinxue Chen, Shermo: A general code for calculating molecular thermodynamic properties, Comput. Theor. Chem., 1200, 113249 (2021) DOI: 10.1016/j.comptc.2021.113249

Loading running parameters from settings.ini...

Running parameters:
Printing individual contribution of vibration modes: No
Temperature:    298.150 K
Pressure:       1.000 atm
Scale factor of vibrational frequencies for ZPE:       1.0000
Scale factor of vibrational frequencies for U(T)-U(0):  1.0000
Scale factor of vibrational frequencies for S(T):    1.0000
Scale factor of vibrational frequencies for CV:       1.0000
Low frequencies treatment: Grimme's interpolation for entropy
Vibrational frequency threshold used in the interpolation is 100.00 cm^-1
Error: Unable to find /home/test123/calculation/6molclus112/6R_04_freq_gau00*.out
Press ENTER button to exit program
想问下楼主为什么我直接使用这个脚本时产生的6R_xx_xxxx_gau00*.out会被删掉（报错是找不到（尝试重新计算频率时发现算好的nmr和ecd文件又被删掉了，想问下是为什么
经过测试好像是每一步开始的时候这些输出文件会被删掉，看了一眼脚本代码也没发现什么可能会删掉这些文件的部分（搞不懂

欢乐多 · 发表于 Post on 2024-5-9 23:45:16

本帖最后由欢乐多于 2024-5-9 08:01 编辑

niduhz 发表于 2024-5-8 20:35
Energy and geometry of all successful configurations have been collectively outputted to isomers.xyz ...

这是molclus程序删掉的，每次运行前都会检查当前文件的.out，并删除，所以最新的6molcus112脚本多了一步将产生的out转变log，以避开molclus的清理作业。

niduhz · 发表于 Post on 2024-5-10 14:37:54

欢乐多发表于 2024-5-9 23:45
这是molclus程序删掉的，每次运行前都会检查当前文件的.out，并删除，所以最新的6molcus112脚本多了一步 ...

明白了，感谢感谢，但是看起来只有度盘链接那个例子里面的6molclus112做了这个更改，感觉楼主可以更新一下附件里的版本（？

欢乐多 · 发表于 Post on 2024-5-11 04:28:18

niduhz 发表于 2024-5-9 22:37
明白了，感谢感谢，但是看起来只有度盘链接那个例子里面的6molclus112做了这个更改，感觉楼主可以更新一 ...

好的

chinchilla · 发表于 Post on 2024-10-11 15:51:46

我把NMR计算那段注释掉，只计算ECD可以吗

欢乐多 · 发表于 Post on 2024-10-12 02:40:47

chinchilla 发表于 2024-10-10 23:51
我把NMR计算那段注释掉，只计算ECD可以吗

可以的

chinchilla · 发表于 Post on 2024-10-12 13:39:34

欢乐多发表于 2024-10-12 02:40
可以的

感谢！

Duoo · 发表于 Post on 2024-10-19 15:12:19

请问TJ老师,这个流程的第三步,优化结构似乎没有带溶剂么?但是溶剂对于结构优化不是也影响挺大的么?如果我们NMR和ECD测试的溶剂不一样的情况下是不是需要修改第三步分别用两个溶剂去优化构象供后续调用呢?
另外请问各位老师如果是在超算集群上进行工作的话,如何修改配置以增加应用上述程序时的计算速度呢?我尝试增加节点数目,但是似乎没有变化.
#SBATCH --nodes=1 #增加到10计算时间没有变化
#SBATCH --ntasks-per-node=16

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[Molclus] chatGPT辅助生成molclus懒人脚本：一键完成对复杂天然产物NMR和ECD计算

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