diogomart
commented
4 weeks ago The atom types are correct, it's just that Vina GPU, which is not developed by us, doesn't support flexible macrocycles. Vina and autodock-gpu, which are developed by us, support flexible macrocycles. For Vina GPU you'll need to disable flexible macrocycles with --rigid_macrocycles
aashuph16221
Hello,
I am working on a ligand library that I generated using Meeko, and I am using AutoDock Vina (GPU version) for docking. However, I am encountering an issue with some of the ligands in the PDBQT files.
In particular, the ligands contain the following non-standard atom types: CG1,G1,G0,G When I run AutoDock Vina, it raises errors about these atom types and cancels the job. Here is an ligand files for reference:
REMARK SMILES Cc1cc(S(=O)(=O)N2C[C@@H]3COCC@HN@H+C3)c(C)s1 REMARK SMILES IDX 18 1 10 2 9 4 8 5 5 6 6 7 7 8 4 9 19 10 3 11 21 12 20 13 REMARK SMILES IDX 2 14 1 15 15 16 16 18 17 19 14 21 13 23 12 24 11 25 REMARK H PARENT 16 20 REMARK Flexibility Score: 160.00 ROOT ATOM 1 C UNL 1 -2.300 0.935 -0.798 1.00 0.00 0.269 C ENDROOT BRANCH 1 2 ATOM 2 C UNL 1 -2.092 0.900 0.733 1.00 0.00 0.085 CG1 ATOM 3 G UNL 1 -3.084 -0.037 1.465 1.00 0.00 0.000 G1 BRANCH 2 4 ATOM 4 C UNL 1 -0.607 0.657 1.100 1.00 0.00 0.114 C BRANCH 4 5 ATOM 5 N UNL 1 -0.175 -0.745 0.932 1.00 0.00 -0.191 NA BRANCH 5 6 ATOM 6 S UNL 1 1.503 -0.899 1.402 1.00 0.00 0.244 S ATOM 7 O UNL 1 1.920 -2.341 1.318 1.00 0.00 -0.207 OA ATOM 8 O UNL 1 1.657 -0.461 2.832 1.00 0.00 -0.207 OA BRANCH 6 9 ATOM 9 C UNL 1 2.560 0.098 0.394 1.00 0.00 0.096 A ATOM 10 C UNL 1 3.243 -0.342 -0.745 1.00 0.00 0.022 A ATOM 11 C UNL 1 2.784 1.454 0.678 1.00 0.00 0.037 A ATOM 12 S UNL 1 4.111 0.953 -1.381 1.00 0.00 -0.145 S ATOM 13 C UNL 1 3.282 -1.727 -1.307 1.00 0.00 0.058 C ATOM 14 C UNL 1 3.641 2.073 -0.222 1.00 0.00 0.003 A ATOM 15 C UNL 1 4.005 3.520 -0.230 1.00 0.00 0.056 C ENDBRANCH 6 9 ENDBRANCH 5 6 BRANCH 5 16 ATOM 16 C UNL 1 -0.372 -1.261 -0.434 1.00 0.00 0.170 CG0 ATOM 17 G UNL 1 -1.871 -1.537 -0.770 1.00 0.00 0.000 G0 ENDBRANCH 5 16 ENDBRANCH 4 5 ENDBRANCH 2 4 ENDBRANCH 1 2 BRANCH 1 18 ATOM 18 N UNL 1 -2.568 -0.386 -1.415 1.00 0.00 -0.332 N ATOM 19 C UNL 1 -2.279 -0.330 -2.863 1.00 0.00 0.333 C ATOM 20 H UNL 1 -3.601 -0.551 -1.354 1.00 0.00 0.348 HD BRANCH 18 21 ATOM 21 C UNL 1 -1.871 -1.537 -0.770 1.00 0.00 0.225 CG0 ATOM 22 G UNL 1 -0.372 -1.261 -0.434 1.00 0.00 0.000 G0 BRANCH 21 23 ATOM 23 C UNL 1 -2.688 -2.101 0.430 1.00 0.00 0.226 C BRANCH 23 24 ATOM 24 O UNL 1 -2.576 -1.346 1.621 1.00 0.00 -0.375 OA BRANCH 24 25 ATOM 25 C UNL 1 -3.084 -0.037 1.465 1.00 0.00 0.171 CG1 ATOM 26 G UNL 1 -2.092 0.900 0.733 1.00 0.00 0.000 G1 ENDBRANCH 24 25 ENDBRANCH 23 24 ENDBRANCH 21 23 ENDBRANCH 18 21 ENDBRANCH 1 18 TORSDOF 2
Is there an option in Meeko to automatically correct these atom types during PDBQT generation? Any guidance you can provide would be greatly appreciated!
Thank you in advance.
Regards,
Ashish