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Error using dabble #18

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Lrolmar opened this issue Dec 16, 2020 · 0 comments
Open

Error using dabble #18

Lrolmar opened this issue Dec 16, 2020 · 0 comments

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@Lrolmar
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Lrolmar commented Dec 16, 2020

Hello!

I have tried to apply your program to several kind of proteins (directly downloaded from the PDB) and the same error raises once and again. I would really appreciate your help.

dabble -i outward_state_n.pdb -o outward_membrane.prmtop -ff charmm36m

Solvent patch dimensions are 44.47 x 44.47 x 210.87
Loading and orienting the solute...
Computing the size of the input periodic cell...
	Solute x diameter is 56.08 (57.03 in TM region)
	Solute y diameter is 45.56 (42.49 in TM region)
	Solute + membrane Z diameter is 60.01
Final system will be 96.08 x 85.56 x 100.56
	X,Y solvent buffer: (40.0, 40.0)
	X,Y transmembrane buffer: (39.1, 43.1)
	Z solvent buffer: 40.5
Tiling solvent...
Traceback (most recent call last):
  File "/home/lroldan/miniconda3/envs/membranes/bin/dabble", line 228, in <module>
    builder.write()
  File "/home/lroldan/miniconda3/envs/membranes/lib/python3.6/site-packages/Dabble/builder.py", line 242, in write
    final_id = self._build()
  File "/home/lroldan/miniconda3/envs/membranes/lib/python3.6/site-packages/Dabble/builder.py", line 162, in _build
    allow_z_tile=self.water_only)
  File "/home/lroldan/miniconda3/envs/membranes/lib/python3.6/site-packages/Dabble/builder.py", line 1088, in tile_membrane_patch
    tmp_dir=tmp_dir)
  File "/home/lroldan/miniconda3/envs/membranes/lib/python3.6/site-packages/Dabble/molutils.py", line 446, in tile_system
    atomsel('all', molid=input_id).set('resid', new_resid)
ValueError: sequence passed to set contains the wrong type of data (integer, float, or str)
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