ADL: Use crystal structure with ligand as reference for docked ligands?
olausson at gmail.com
Wed Mar 26 17:14:10 PDT 2008
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.
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