MDTraj
Installation
New to Python
Examples
What’s New?
Trajectory Reference
Analysis Reference
Atom Selection Reference
Low-level API
OpenMM Reporters
MDTraj Utils
mdconvert
MDTraj HDF5 Format Specification
MDTraj
Calculating NMR observables with
mdtraj.nmr()
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Calculating NMR observables with
mdtraj.nmr()
An error occurred while executing the following cell: ------------------ shifts = md.nmr.chemical_shifts_spartaplus(trj) shifts[0:10] ------------------ [31m---------------------------------------------------------------------------[39m [31mOSError[39m Traceback (most recent call last) [36mCell[39m[36m [39m[32mIn[3][39m[32m, line 1[39m [32m----> [39m[32m1[39m shifts = md.nmr.chemical_shifts_spartaplus(trj) [32m 2[39m shifts[[32m0[39m:[32m10[39m] [36mFile [39m[32m~/checkouts/readthedocs.org/user_builds/mdtraj/envs/latest/lib/python3.13/site-packages/mdtraj/nmr/shift_wrappers.py:303[39m, in [36mchemical_shifts_spartaplus[39m[34m(trj, rename_HN)[39m [32m 301[39m binary = find_executable(SPARTA_PLUS) [32m 302[39m [38;5;28;01mif[39;00m binary [38;5;129;01mis[39;00m [38;5;28;01mNone[39;00m: [32m--> [39m[32m303[39m [38;5;28;01mraise[39;00m [38;5;167;01mOSError[39;00m( [32m 304[39m [33mf[39m[33m"[39m[33mExternal command not found. Looked for [39m[38;5;132;01m{[39;00mSPARTA_PLUS[38;5;132;01m}[39;00m[33m in PATH. [39m[33m"[39m [32m 305[39m [33m"[39m[33m`chemical_shifts_spartaplus` requires the external program SPARTA+, available at [39m[33m"[39m [32m 306[39m [33m"[39m[33mhttp://spin.niddk.nih.gov/bax/software/SPARTA+/[39m[33m"[39m, [32m 307[39m ) [32m 309[39m names = [ [32m 310[39m [33m"[39m[33mresSeq[39m[33m"[39m, [32m 311[39m [33m"[39m[33mresName[39m[33m"[39m, [32m (...)[39m[32m 318[39m [33m"[39m[33mSIGMA[39m[33m"[39m, [32m 319[39m ] [32m 321[39m [38;5;28;01mwith[39;00m enter_temp_directory(): [31mOSError[39m: External command not found. Looked for ['sparta+', 'SPARTA+', 'SPARTA+.linux'] in PATH. `chemical_shifts_spartaplus` requires the external program SPARTA+, available at http://spin.niddk.nih.gov/bax/software/SPARTA+/
(
nmr.ipynb
;
nmr_eval.ipynb
;
nmr.py
)