Hi all,
I am dealing with the docking of B1 with LibDock. As you know, the first step of LibDock is generateing diverse conformations. This protocol itself is quite easy to use but I still failed...I cannot generate mutiple conformations for B12 since there is a Co(cobalt) atom in the central corrin ring. The bond order of the central Co is 5 which does not meet the requirement of the Valency checking of Catalyst. Below is the the Wanning information given by DS:
By the way, you can find the B12 pdb file in the attachment if you want you test it yourself. Besides, I do not add any H atom in that PDB. If you add H atom yourself and put a Valence monitor on it, you will find out there are 4 Valence wannings. Three for three C atoms whose bond order is 3, and one for the Co atom whose bond order is 5. Oh, I almost forget, B12 can not pass the Ligand Prepare protocol either.
Anybody can fix this? Thanks in advance.
WARNING: Valency requirements on Co1 cannot be met. (Bond order = 5 and formal charge = 0.
WARNING: bad valency detected at atom 1.
1 failed compounds written to Program Files\SciTegic\web\jobs\Knight\{clp35B1A-63FA-4FFA-AD73-274C65950C31}/Intermediate/confgen_fail.sd
I am dealing with the docking of B1 with LibDock. As you know, the first step of LibDock is generateing diverse conformations. This protocol itself is quite easy to use but I still failed...I cannot generate mutiple conformations for B12 since there is a Co(cobalt) atom in the central corrin ring. The bond order of the central Co is 5 which does not meet the requirement of the Valency checking of Catalyst. Below is the the Wanning information given by DS:
By the way, you can find the B12 pdb file in the attachment if you want you test it yourself. Besides, I do not add any H atom in that PDB. If you add H atom yourself and put a Valence monitor on it, you will find out there are 4 Valence wannings. Three for three C atoms whose bond order is 3, and one for the Co atom whose bond order is 5. Oh, I almost forget, B12 can not pass the Ligand Prepare protocol either.
Anybody can fix this? Thanks in advance.
WARNING: Valency requirements on Co1 cannot be met. (Bond order = 5 and formal charge = 0.
WARNING: bad valency detected at atom 1.
1 failed compounds written to Program Files\SciTegic\web\jobs\Knight\{clp35B1A-63FA-4FFA-AD73-274C65950C31}/Intermediate/confgen_fail.sd
