ADL: Use crystal structure with ligand as reference for docked ligands?

Bjoern Olausson olausson at
Wed Mar 26 17:14:10 PDT 2008

Hi community,

I am new to AutoDock and trying to validate this method for my needs.

The dockings are working fine and everything seems fine.

But how do I get a RMS?

- Got a crystal structures from a protein as apo-protein and complexed with a 

- Docked the same ligand as found in the complexed crystal structure into the 

- Analyzing the results shows a big cluster (35/50)

But how do I set/select the ligand from the complexed structure as reference 
to calculate the RMS?

Should I run the docking with the complexed structure? If thou, what to do 
with the ligand in the structure? Dos it interfere with the docking process?

I could not find a thing about the RMS in the FAQs and or tutorials.

All in all, I just want to know if it is possible to use a crystal structure 
with a ligand as reference for my "AutoDocked" ligands.

Any hint/tip is wellcome

Thanks and regards

There is nothing in this world
that does not have its decisive moment.

Henri Cartier-Bresson
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