Open jintianyun56 opened 10 months ago
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.
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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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.
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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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.
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.
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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