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mdtraj / mdtraj

An open library for the analysis of molecular dynamics trajectories
https://mdtraj.readthedocs.io/en/latest/
GNU Lesser General Public License v2.1
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How should I add SPARTA+ available on my mac path for NMR chemical shift analysis? #1729

Open TianmingQu opened 2 years ago

TianmingQu commented 2 years ago

FYI, I add the following words (export PATH="/Users/TMQ/Desktop/QTMproject/SPARTA/SPARTA+:${PATH}") to my .bash_profile and source it, but still the

"md.chemical_shifts_spartaplus(t,rename_HN=True)" function does not work and shows the following error:

OSError Traceback (most recent call last)

in ----> 1 cs = md.chemical_shifts_spartaplus(t,rename_HN=True) ~/opt/anaconda3/lib/python3.8/site-packages/mdtraj/nmr/shift_wrappers.py in chemical_shifts_spartaplus(trj, rename_HN) 274 binary = find_executable(SPARTA_PLUS) 275 if binary is None: --> 276 raise OSError('External command not found. Looked for %s in PATH. `chemical_shifts_spartaplus` requires the external program SPARTA+, available at [http://spin.niddk.nih.gov/bax/software/SPARTA+/'](http://spin.niddk.nih.gov/bax/software/SPARTA+/'%3C/span%3E) % ', '.join(SPARTA_PLUS)) 277 278 names = ["resSeq", "resName", "name", "SS_SHIFT", "SHIFT", "RC_SHIFT", "HM_SHIFT", "EF_SHIFT", "SIGMA"] OSError: 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+/ Could someone help me with how to add the path correctly?
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