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Acellera / htmd

HTMD: Programming Environment for Molecular Discovery
https://software.acellera.com/docs/latest/htmd/index.html
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unable to execute the tutorial #1089

Closed pritam0070 closed 3 months ago

pritam0070 commented 7 months ago

ModuleNotFoundError: No module named 'aceprep'

During handling of the above exception, another exception occurred:

RuntimeError Traceback (most recent call last) Cell In[16], line 1 ----> 1 prot = systemPrepare(prot, pH=7.0)

pritam0070 commented 7 months ago

BuildError Traceback (most recent call last) Cell In[29], line 2 1 from htmd.home import home ----> 2 tryp_charmm = charmm.build(tryp_solv, outdir='build-charmm')

File ~/mambaforge/envs/htmd/lib/python3.9/site-packages/htmd/builder/charmm.py:394, in build(mol, topo, param, stream, prefix, outdir, caps, ionize, saltconc, saltanion, saltcation, disulfide, regenerate, patches, noregen, aliasresidues, psfgen, execute, _clean) 392 molbuilt.read(path.join(outdir, "structure.psf")) 393 else: --> 394 raise BuildError( 395 "No structure pdb/psf file was generated. Check {} for errors in building.".format( 396 logpath 397 ) 398 ) 400 if ionize: 401 os.makedirs(path.join(outdir, "pre-ionize"))

BuildError: 'No structure pdb/psf file was generated. Check /home/pk/Documents/MD_HTMD/build-charmm/log.txt for errors in building.'

stefdoerr commented 6 months ago

Hi, for the first error you will have to either mutate or remove the non-canonical residues in your protein. AcePrep is only available in the commercial version and allows preparation of non-canonical residues.

As for the second error please attach the log.txt which the error mentions.

stefdoerr commented 3 months ago

Closing due to inactivity