ADL: autodock_element field
rhuey at scripps.edu
Mon Mar 31 09:01:16 PDT 2008
After removing the water molecules, you should add all hydrogens to your
[Use the default 'All Hydrogens' and 'noBondOrder']
Next, you can use the ADT menu
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
(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
for more information.
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.
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