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forlilab / waterkit

Tool to predict water molecules placement and energy in ligand binding sites
GNU General Public License v3.0
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wk_prepare_receptor.py failed #3

Closed zhentg closed 10 months ago

zhentg commented 1 year ago

python ../scripts/wk_prepare_receptor.py -i 7u9y_pro.pdb -o 7u9y_pro_prep --pdb --amber_pdbqt Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. INFO:WaterKit receptor preparation:Removed all hydrogen atoms INFO:WaterKit receptor preparation:Removed all water molecules Traceback (most recent call last): File "/tools/solvation/waterkit-master/test/../scripts/wk_prepare_receptor.py", line 854, in main() File "/tools/solvation/waterkit-master/test/../scripts/wk_prepare_receptor.py", line 838, in main pr.prepare(pdb_filename, lib_files, frcmod_files, clean) File "/tools/solvation/waterkit-master/test/../scripts/wk_prepare_receptor.py", line 655, in prepare ns_names = _find_non_standard_resnames(pdbfixer.parm, AMBER_SUPPORTED_RESNAMES + nonstandard_resnames) TypeError: can only concatenate tuple (not "list") to tuple

7u9y_pro.zip

jeeberhardt commented 1 year ago

Hi @zhentg,

Sorry, last minute untested modifications... it is now fixed!

zhentg commented 1 year ago

Hi @jeeberhardt ,

Thanks for the bug fix. After update whole waterkit directory, now the output seems correct. Is it necessary to correct the 'simtk.openmm' importing statement?

Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. INFO:WaterKit receptor preparation:Removed all hydrogen atoms INFO:WaterKit receptor preparation:Removed all water molecules WARNING:WaterKit receptor preparation:Histidine protonation will be automatically assigned to HIE: HIS - 44, HIS - 86, HIS - 128, HIS - 170, HIS - 178, HIS - 255, HIS - 300, HIS - 310