charmm build in htmd 2.3.8

[shozebhaider]

Hi,

I am using htmd 2.3.8. I think there is some issue with the charmm build in your latest release. I keep getting the error (see below). The log.txt file is also empty. The notebook I am using is your system-building-protein-protein.ipynb tutorial. The notebook is also attached.

system-building-protein-protein.zip

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BuildError Traceback (most recent call last) Cell In[15], line 1 ----> 1 molbuilt = charmm.build(smol, outdir='./build/')

File ~/miniconda3/envs/htmd/lib/python3.10/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/shozeb/Downloads/build/log.txt for errors in building.

[shozebhaider]

Just to add another observation. This charmm build works on Ubuntu 20.04 but not on 22.x

[stefdoerr]

Indeed it works on my machine which is 20.04. I would suggest doing conda list with your env activated on both machines and doing a diff of the packages which are installed on the two envs. I assume one will have different version of psfgen. Either that or the build of psfgen links to something which doesn't exist in Ubuntu 22.x. You could do which psfgen and ldd on that path to see if there are any missing linked libraries. Doesn't seem to be related to HTMD though as far as I can tell

[shozebhaider]

@stefdoerr sure..let me look deeper into this. Clearly not related to htmd but would be good for users to know why charmm build doesnt work on Ubuntu 22.x