Hi Kanika, Take a look at the ViewDock tutorial. It looks at H-bonds between ligand and receptor using the FindHBond tool. <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/tutorials/vdtut.html> <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/findhbond/f...> Another tool that might be useful for this purpose is Find Clashes/Contacts (in menu under Tools... Surface/Binding Analysis): <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/findclash/f...> I also recommend doing the Structure Analysis and Comparison tutorial, which uses distance measurements, FindHBond, Find Clashes/Contacts etc. to examine a binding pocket: <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/tutorials/squalene.h...> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Feb 18, 2013, at 3:34 AM, kanika sharma wrote:
Hi All, I docked a drug to a protein structure using Autodock Vina. To view the result, I am using View Dock. I now have 5 positions in which the drug is docked into the protein. Is there a way to figure out which residues in the protein are interacting with the drug molecule at each position? -- Regards, Kanika Sharma