Closed SynchronyML closed 1 year ago
Hi, the PDBQT does not set bonds, so Pymol is guessing them based on distances. The bonds in the five-member ring in the SDF you posted may be a little short.
Thanks for your suggestion, it is indeed the problem of imp small molecule five-membered ring. But here I found that the five-membered ring in pdbqt can be perfectly converted to sdf format using obabel.
OpenBabel also has to guess bonds and bond orders, which is an impossible task for some molecules. It is safer to use mk_copy_coords.py
(which we will rename to mk_export.py
in meeko v0.4.0).
Hello, when I tried to use Meeko to convert IMP.sdf to pdbqt format for input vina docking, I found that Meeko could not complete the ring conversion correctly. I would appreciate it if you could help me!
Below is the sdf file of imp