list index out of range

[jintianyun56]

Hi Prof. Anan,

It showed "list index out of range" when I run the evanmr2.py . also show "Explicit valence for atom # 23 N, 4, is greater than permitted"

Would you like to help me to find something to troubleshoot?

Thanks

[Anan-Wu-XMU]

Could you please check whether there are data in allNMR and allHNMR, in which calculated 13C/1H chemical shieldings are collected. evanmr2.py read relevant data from allNMR/allHNMR, freeG.txt and automatically evaluate the Boltzmann averaged 13C/1H chemical shifts, which will be stored in avNMR.txt and avHNMR.txt, respectively. It looks to me that there are problems in NMR calculations or possibly geometry optimizations.

[jintianyun56]

Thanks, Yes, avNMR.txt and avHNMR.txt were blank. I'll try to make it work.

Anan-Wu-XMU @.***> 于2023年12月10日周日 17:08写道：

Could you please check whether there are data in allNMR and allHNMR, in which calculated 13C/1H chemical shieldings are collected. evanmr2.py read relevant data from allNMR/allHNMR, freeG.txt and automatically evaluate the Boltzmann averaged 13C/1H chemical shifts, which will be stored in avNMR.txt and avHNMR.txt, respectively. It looks to me that there are problems in NMR calculations or possibly geometry optimizations.

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[Anan-Wu-XMU]

A success run will generate files as shown in the following figure, in which

  *.sdf :   input conformers 
  *geom?.com/log:   geometry optimization files
  *geom?.new:   optimized geometries
  *geom-NMR.com/log:   xOPBE NMR calculation files
  *geom?-NMR.NMR:  calculated 13C chemical shieldings of individual conformer
  *geom?-NMR.HNMR: calculated 1H chemical shieldings of individual conformer 
  allNMR/allHNMR:   collected chemical shieldings for all valid conformers (< 10kj/mol)
  avNMR.txt:    the Boltzmann averaged 13C chemical shifts
  avHNMR.txt:   the Boltzmann averaged 1H chemical shifts 

Thanks, Yes, avNMR.txt and avHNMR.txt were blank. I'll try to make it work.

[jintianyun56]

Thanks, The example ran well, and I am trying my structure. I am wondering about why we don't assign the chemical shit to the carbon number. the svm method only sequences the chemical shift from small to big, as experiments C2: 132, C3 134, if case 1 calculation C2:134, C3: 132,; case 2 cal. C2:132, C3: 134. I think the SVM-M method is hard to identify case 1 and 2.

Anan-Wu-XMU @.***> 于2023年12月11日周一 17:28写道：

A success run will generate files as shown in the following figure, in which

.sdf : input conformers geom?.com/log: geometry optimization files geom?.new: optimized geometries geom-NMR.com/log: xOPBE NMR calculation files geom?-NMR.NMR: calculated 13C chemical shieldings of individual conformer geom?-NMR.HNMR: calculated 1H chemical shieldings of individual conformer allNMR/allHNMR: collected chemical shieldings for all valid conformers (< 10kj/mol) avNMR.txt: the Boltzmann averaged 13C chemical shifts avHNMR.txt: the Boltzmann averaged 1H chemical shifts

2023-12-12.091306.jpg (view on web) https://github.com/Anan-Wu-XMU/SVM-M/assets/89952471/1a36232d-4343-4649-9055-c650ea99bd70

Thanks, Yes, avNMR.txt and avHNMR.txt were blank. I'll try to make it work.

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[Anan-Wu-XMU]

Indeed, case 1 and 2 are identical within the framework of SVM-M method. As stated in our paper, the sorting is to avoid the mis-assignment in experiments and make the model applicable when only unassigned data are available. We are currently working on a 2D method based on SVM-M, which can handle 2D NMR data. The atomic labelling are important and taken in consideration in this method.

Thanks, The example ran well, and I am trying my structure. I am wondering about why we don't assign the chemical shit to the carbon number. the svm method only sequences the chemical shift from small to big, as experiments C2: 132, C3 134, if case 1 calculation C2:134, C3: 132,; case 2 cal. C2:132, C3: 134. I think the SVM-M method is hard to identify case 1 and 2.

[jintianyun56]

Thanks, I am looking forward to the new 2D method.

Anan-Wu-XMU @.***> 于2023年12月11日周一 23:31写道：

Indeed, case 1 and 2 are identical within the framework of SVM-M method. As stated in our paper, the sorting is to avoid the mis-assignment in experiments and make the model applicable when only unassigned data are available. We are currently working on a 2D method based on SVM-M, which can handle 2D NMR data. The atomic labelling are important and taken in consideration in this method.

Thanks, The example ran well, and I am trying my structure. I am wondering about why we don't assign the chemical shit to the carbon number. the svm method only sequences the chemical shift from small to big, as experiments C2: 132, C3 134, if case 1 calculation C2:134, C3: 132,; case 2 cal. C2:132, C3: 134. I think the SVM-M method is hard to identify case 1 and 2.

— Reply to this email directly, view it on GitHub https://github.com/Anan-Wu-XMU/SVM-M/issues/3#issuecomment-1851441987, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANDXOWC5VCUBCLZIXZLRRO3YJAB5XAVCNFSM6AAAAABAOWKY3OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJRGQ2DCOJYG4 . You are receiving this because you authored the thread.Message ID: @.***>