ADL: Adding extra atom in autodock

Austin B. Yongye ybausty at
Wed Apr 18 06:56:03 PDT 2007

Hi everyone,
I added a new atom type 'X' in my ligand when
preparing the .pdbq input file.
1. I saved the .pdbq file and ran the autogrid
calculation. But when I do the command:
Docking -> Set Ligand Parameters -> Choose Ligand,
Autodock gets only atom types CNOH, not CNOHX.

2. If I save the .dpf and manually enter the
Lennard-Jones 12-6 parameters for atom type X, I get
this error message when I run autodock:
WARNING!  Atom type error, can't find type for "BD" in
typelist "CNOHX"

3. If I go back to my initial ligand.pdb file, and
change BD to X, autodock tools gripes about X not
being an element.

I am sure people have run docking simulations with
extra atom types. Any help would be greatly

Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 

More information about the autodock mailing list