ADL: Could anyone help me please??

Normandé Morrison normandemorrison at
Fri Nov 18 10:53:25 PST 2011

I've used autodock to generate some pdbqts before, yet this time, I'm using a resulting pdb from a molecular dynamics simulation (NAMD). During this simulation, one of the commands is to change HIS to HSE... so I thought this could be the error, and though I've changed it back to HIS on the pdb, I'm still getting several errors while trying to generate my pdbqt.

When I try to add the polar hydrogens, an error message appears telling me that it could not find an atomic number for M M.
Another series of errors is when I'm trying to choose this pdb as the macromolecule, using Grid (autodock tools). It tells me that some charges need to be corrected on the written pdb file. If I overlook this and proceed to save the macromolecule as a pdbqt file, it tells me: could not create the file, all atoms do not have an autodock_element field... This error comes even after trying to assing the AD4 element (edit --> atoms --> assign AD4 type), as well as merging non-polar hydrogens. When overlooking this too, a window appears, indicating that HG1, HE2, HH1, HH2, HD2... etc do not have a charge.

So, the only difference is that I'm using a pdb generated from a molecular dynamics simulation, and yet I don't know what to do to correct all these errors... 

.Normandé Morrison. 


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