Closed luwei0917 closed 2 years ago
Hello, I'm trying to convert SDF file into pdbqt format using following command:
mk_prepare_ligand.py -I a.sdf -o a.pdbqt --pH 7.4
But my a.pdbqt file contains sometime I don't understand:
ATOM 27 G UNL 1 -0.000 -4.585 0.000 1.00 0.00 0.000 G0
what is this atom G? will this affect further docking?
a.sdf is copied below.
RDKit 2D 25 28 0 0 0 0 0 0 0 0999 V2000 -5.1962 -13.5850 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 -3.8971 -12.8350 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -13.5850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2990 -12.8350 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2990 -11.3350 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -10.5850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8971 -11.3350 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -9.0850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2990 -8.3350 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -9.0850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -10.5850 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2990 -6.8350 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -6.0850 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -4.5850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3515 -3.9342 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6852 -2.4718 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6852 -2.4718 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.3515 -3.9342 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5242 -4.8694 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 3 4 1 0 4 5 2 0 5 6 1 0 6 7 2 0 6 8 1 0 8 9 2 0 9 10 1 0 10 11 1 0 9 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 2 0 18 19 1 0 19 20 1 0 20 21 2 0 18 22 1 0 22 23 2 0 23 24 1 0 24 25 2 0 7 2 1 0 20 14 1 0 11 5 1 0 25 17 1 0 M END
Thanks!
Hello,
G atoms are for macrocycles. See: https://autodock-vina.readthedocs.io/en/latest/docking_macrocycle.html
thanks a lot!
Hello, I'm trying to convert SDF file into pdbqt format using following command:
mk_prepare_ligand.py -I a.sdf -o a.pdbqt --pH 7.4
But my a.pdbqt file contains sometime I don't understand:
ATOM 27 G UNL 1 -0.000 -4.585 0.000 1.00 0.00 0.000 G0
what is this atom G? will this affect further docking?
a.sdf is copied below.
Thanks!