AMBER Archive (2007)

Subject: AMBER: Targeted MD

From: Beale, John (jbeale_at_stlcop.edu)
Date: Sat Sep 08 2007 - 17:29:08 CDT

I would like to perform targeted MD on a series of small molecule ligands and their protein receptors. I have created the complete set of files for the ligands with antechamber, and have built the pdb files of the complexes of the ligands bound to the protein sites. It isn't clear to me what to do next. Can someone please give me a stepwise set of instructions that will point me in the right direction? For instance, what additional datasets do I need to perform the targeted MD docking procedures?
 
Thank you very much!
 
John
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