ADL: oxygen atom found with no bonded atoms

mostafa_ jm mostafa_mj at yahoo.com
Fri Jun 28 10:59:42 PDT 2013


Dear All
I've been trying to dock a ligand in an enzyme which has Mg atom and co-factors, However, when I run autogrid4.2 I receive these following
messages:
WARNING:  Oxygen atom found with no bonded atoms, atom serial number 4322, atom_type 6
WARNING:  Oxygen atom found with no bonded atoms, atom serial number 4323, atom_type 6
WARNING:  Oxygen atom found with no bonded atoms, atom serial number 4324, atom_type 6
WARNING:  Oxygen atom found with no bonded atoms, atom serial number 8646, atom_type 6
WARNING:  Attempt to divide by zero was just prevented
I've checked the pdbqt file and atoms 4322, 4323, 4324 are oxygen of gtp co-factor and atom 8646 is oxygen of gdp co-factor.
before this I had done the followings:
-opened protein pdb file 
-removed water molecules and the irreversible ligand
-repair its missed residues and optimized it
-added all hydrogen atoms 
-saved it as pdbqt (when I was saving this file I faced the message which said there is no charge on Mg atom then I added the relative charge directly on the Mg atom in pdbqt file)
-run autogrid4 
could anyone please explain to me why I get these warnings?
Any help will be much appreciated.

Thank you!
javaheri


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