ADL: Docking issue

Sebastian Fica smfica at uchicago.edu
Thu Jan 15 06:51:47 PST 2009


Hi,

I am trying to use Autodock to dock an RNA hairpin on a protein and  
when I do simulated annealing (I started with SA because it runs very  
fast, but maybe it's the wrong algorithm) the result is that my RNA  
basically gets superimposed on the center of the protein rather than  
being docked. I was wondering if anybody might know what the issue  
could be. I was thinking that part of the problem is that when I  
calculated the gpf file I had it centered on the protein because I did  
not know how to write the syntax for centering it on a specific atom,  
so if someone could let me know how to do that it would be appreciated.

Kind of related to this, I was wondering if there is some way to do  
the docking so that I can keep two Mg atoms present in the RNA crystal  
structure and have them interact with a specific residue in the protein.

Thanks,
Sebastian


Sebastian M. Fica
Graduate Student, Staley Laboratory
Department of Molecular Genetics and Cell Biology
The University of Chicago
920 E. 58th St., Chicago, IL 60637
Lab Phone: 773-834-5885












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