ADL: Adding extra atom in autodock

Austin B. Yongye ybausty at yahoo.com
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
appreciated.
Thanks,
Austin-

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