Closed AKBforever closed 2 years ago
The atom indexing is 0-based. The atom number 1 is the sodium (Na) for which there are no PDBQT parameters, so the file cannot be generated. (In general it is not a good practice to dock molecules in a salt form, unless you really know what you're doing).
I'm going to close the issue, but feel free to reopen it if you think there are other problems.
Besides the Na, the 2D depiction is wrong in https://pubchem.ncbi.nlm.nih.gov/compound/101095070
I want to transfer an sdf file of a molecule (PubChem CID: 101095070) to a pdbqt file,but mk_prepare_ligand.py did not work.
The sdf file of 101095070, which was transferred to 3D by MOE, is: 101095070 MOE2020 3D
26 24 0 0 1 0 0 0 0 0999 V2000 2.1840 -0.8960 0.1650 S 0 0 0 0 0 0 0 0 0 0 0 0 8.4960 -1.4980 2.1000 Na 0 3 0 0 0 0 0 0 0 0 0 0 1.0770 0.1120 -0.1200 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2500 -1.1240 1.5630 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0560 -2.0330 -0.6730 O 0 0 0 0 0 0 0 0 0 0 0 0 9.4960 0.1660 1.2030 O 0 5 0 0 0 0 0 0 0 0 0 0 7.3940 -0.0910 0.5940 N 0 0 0 0 0 0 0 0 0 0 0 0 5.0350 -0.6660 0.1490 C 0 0 3 0 0 0 0 0 0 0 0 0 3.6890 -0.0560 -0.3090 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1990 0.2900 -0.1580 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2900 -2.0450 -0.4850 C 0 0 0 0 0 0 0 0 0 0 0 0 8.5120 0.5710 0.5040 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6950 1.7460 -0.3510 C 0 0 0 0 0 0 0 0 0 0 0 0 9.8510 2.4350 -0.4280 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9710 -0.7800 1.2340 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7670 0.0780 -1.3780 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7040 0.9620 0.0490 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9400 1.3050 0.1490 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4350 0.2670 -1.2240 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2680 -1.9700 -1.5740 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5320 -2.7600 -0.1620 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2660 -2.4250 -0.1820 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0280 0.6800 0.6580 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8700 2.0570 -0.9320 H 0 0 0 0 0 0 0 0 0 0 0 0 10.7010 2.1520 0.1390 H 0 0 0 0 0 0 0 0 0 0 0 0 9.9680 3.2820 -1.0520 H 0 0 0 0 0 0 0 0 0 0 0 0 1 3 1 0 0 0 0 1 4 2 0 0 0 0 1 5 2 0 0 0 0 1 9 1 0 0 0 0 3 23 1 0 0 0 0 6 12 1 0 0 0 0 7 10 1 0 0 0 0 7 12 2 0 0 0 0 8 9 1 0 0 0 0 8 10 1 0 0 0 0 8 11 1 0 0 0 0 8 15 1 0 0 0 0 9 16 1 0 0 0 0 9 17 1 0 0 0 0 10 18 1 0 0 0 0 10 19 1 0 0 0 0 11 20 1 0 0 0 0 11 21 1 0 0 0 0 11 22 1 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 13 24 1 0 0 0 0 14 25 1 0 0 0 0 14 26 1 0 0 0 0 M CHG 1 2 1 M CHG 1 6 -1 M END
And the error information was: _Traceback (most recent call last): File "/home/ubuntu/miniconda3/envs/vina/bin/mk_prepare_ligand.py", line 171, in
ligand_prepared = preparator.write_pdbqt_string()
File "/home/ubuntu/miniconda3/envs/vina/lib/python3.9/site-packages/meeko/preparation.py", line 213, in write_pdbqt_string
raise RuntimeError("Molecule not OK, refusing to write PDBQT\n\nLOG:\n%s" % self.log)
RuntimeError: Molecule not OK, refusing to write PDBQT
LOG: atom number 1 has None type, mol name: 101095070_
I noted that the first atom is S, so mk_prepare_ligand.py cannot recognize this atomtype?