That error happens when a norm of a vector is zero, which shouldn't be possible. Do you only get this error for certain inputs? Can you provide the input example?
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Hello,
I am getting this error: 'An internal error occurred in /Users/dkoes/git/smina/src/lib/tree.h(133).' What would be the reason?
Thank you
That error happens when a norm of a vector is zero, which shouldn't be possible. Do you only get this error for certain inputs? Can you provide the input example?
Thanks, David. Below is my command line run in Jupyter Note book: !../smina.osx.12.sh -r {'1X1R_clean_H.pdb'} -l {'InputMols.mol2'} -o {'1X1R_lig_smina_out.sdf'} --center_x 3.4204999953508377 --center_y 9.91599988937378 --center_z 11.27299976348877 --size_x 19.56700000166893 --size_y 18.30399990081787 --size_z 23.20599937438965 --exhaustiveness 8 --num_modes 5.
Do you see any problem with this command?
Thank you
I need the input files. My assumption is there is something broken with the molecules.
Thanks David. Here they are:
smiles=['C1=NC(=C2C(=N1)N(C=N2)CCOCP(=O)(O)O)N',
'C1=NC(=C2C(=N1)N(C=N2)[C@H]3C@@HO)O)N',
'CC@@HC(=O)N1C3=CC=CC=C3)NC4=NC=NC5=C4NC=N5',
'C1=NC(=C2C(=N1)N(C=N2)C3C(C(C(O3)CO)O)O)N',
'CC@HOCP@@(N[C@@H]',
'C1=NC(=C2C(=N1)N(C=N2)[C@H]3C@@HN)N)O)O)N',
'CS+N)C[C@@H]1C@HO)O',
'CN1C=C(C(=N1)OC)NC2=C3C(=NC(=N2)N4CC@HNC(=O)C=C)N(C=N3)C',
'C1COC[C@@H]1NC2=C3C(=NC=N2)N(C=N3)[C@H]4C@@HO)O']
The first three ligdand docked without any problem but docking failed for the 4th ligand with above error.
Those are smiles, not a mol2 or pdb. I need the actual input file that files.