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dauparas / LigandMPNN

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index 0 is out of bounds for dimension 1 with size 0 #18

Open sherryliu987 opened 7 months ago

sherryliu987 commented 7 months ago

Getting an error for LigandMPNN

Traceback (most recent call last): File "/home/ubuntu/LigandMPNN/run.py", line 794, in main(args) File "/home/ubuntu/LigandMPNN/run.py", line 353, in main feature_dict = featurize( ^^^^^^^^^^ File "/home/ubuntu/LigandMPNN/data_utils.py", line 945, in featurize Y, Y_t, Y_m, D_XY = get_nearest_neighbours( ^^^^^^^^^^^^^^^^^^^^^^^ File "/home/ubuntu/LigandMPNN/data_utils.py", line 897, in get_nearest_neighbours D_AB_closest = torch.sqrt(L2_AB_nn[:, 0])


IndexError: index 0 is out of bounds for dimension 1 with size 0
sherryliu987 commented 7 months ago

Am now getting a slightly different error, still out of bounds. My protein only has 193 residues but it seems to be accessing 195? I have not specified any fixed or designed residues.

File "/home/ubuntu/LigandMPNN/data_utils.py", line 509, in get_aligned_coordinates atomcoords[CA_dict[code], :] = atom_coords[i]


IndexError: index 195 is out of bounds for axis 0 with size 193
dauparas commented 6 months ago

Any chance you could share the input PDB so that I can try to replicate this error, please?

kimdn commented 1 month ago

I had the similar error


==> peptide_design_7513421.err <==
Traceback (most recent call last):
  File "/people/kimd999/script/python/design/LigandMPNN/run.py", line 988, in <module>
    main(args)
  File "/people/kimd999/script/python/design/LigandMPNN/run.py", line 393, in main
    feature_dict = featurize(
                   ^^^^^^^^^^
  File "/qfs/people/kimd999/script/python/design/LigandMPNN/data_utils.py", line 946, in featurize
    Y, Y_t, Y_m, D_XY = get_nearest_neighbours(
                        ^^^^^^^^^^^^^^^^^^^^^^^
  File "/qfs/people/kimd999/script/python/design/LigandMPNN/data_utils.py", line 898, in get_nearest_neighbours
    D_AB_closest = torch.sqrt(L2_AB_nn[:, 0])
                              ~~~~~~~~^^^^^^
IndexError: index 0 is out of bounds for dimension 1 with size 0

This error occurred when there is no element notation at end of each line like

ATOM     39  C   GLY A  10     -12.985 -10.409 -16.815  1.00  0.00
ATOM     40  O   GLY A  10     -13.118 -11.007 -15.747  1.00  0.00
HETATM   41  N   LIG    11     -38.288  36.148   5.348  1.00  1.00
HETATM   42  CA  LIG    11     -37.548  34.892   5.336  1.00  1.00

Adding element like


ATOM     39  C   GLY A  10     -12.985 -10.409 -16.815  1.00  0.00           C
ATOM     40  O   GLY A  10     -13.118 -11.007 -15.747  1.00  0.00           O
HETATM   41  N   LIG    11     -38.288  36.148   5.348  1.00  1.00           N
HETATM   42  CA  LIG    11     -37.548  34.892   5.336  1.00  1.00           C
HETATM   43  C   LIG    11     -36.391  34.925   6.329  1.00  1.00           C

solved