ADL: autodock_element field

Ruth Huey rhuey at scripps.edu
Mon Mar 31 09:01:16 PDT 2008


Hi Larry,
After removing the water molecules, you should add all hydrogens to your 
protein via:
Edit->Hydrogens->Add
[Use the default 'All Hydrogens' and 'noBondOrder']

Next, you can use the ADT menu
Grid->Macromolecule->Choose
This will result in adding gasteiger charges, merging non-polar 
hydrogens, adding autodock_elements and opening a file browser for you 
to select  a filename for writing the pdbqt.

IF for some reason, you want to do this step by step:
(1) before adding Gasteiger charges, you should add all hydrogens to 
your protein via
Edit->Hydrogens->Add
(2) after adding Gasteiger charges, you should merge non-polar hydrogens 
to conform to the atom types  supported by AutoDock
Edit->Hydrogens-> Merge Non-Polar
(3) To add an autodock_element, which is the autodock4 atom type, to 
each atom, you can use
Edit->Atoms->Assign AD4 type

See 
/http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file 
for more information.

     Ruth

Larry Layne wrote:
> Greetings all,
>
> I am having trouble saving a protein from the pdb (.pdb) as a .pdbqt file.  I removed the water molecules and attempted to save the file as a .pdbqt so that I can select flexible residues.  My first error required the addition of Kollman or Gasteiger charges, which I did.  Now I am getting an error that reads, "all atoms do not have an autodock_element field."  What is this, and how can I correct it.  
>
> Larry  
>
> ________________________________________________
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>
>   



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