Hi Alex, Chimera does not do MD, so I'm guessing you just want to use it to prepare the structure before doing MD with some other program. You can add bonds with the Build Structure tool (Tools... Structure Editing... Build Structure, go to Add/Delete Bonds tab) or the command "bond," but first you have to combine the receptor and ligand into one model. Chimera will not bond two different models. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#addbond> You can combine the two models with the "combine" command, or by choosing the two models in the lefthand side of the Model Panel (opened from Favorites menu) and then clicking the "copy/combine..." button on the right. That will open a GUI with more settings for generating the new combined model. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#functions> In the combined model, you can add the bond as mentioned above. 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 May 27, 2010, at 6:51 AM, Alex Perálvarez Marín wrote:

Dear all, after running a Docking, I want to build a covalent bond between the receptor and the ligand and then run MD simulations. Is it done with the "build structure" menu? There is another way of doing it? Probably this has been discussed earlier, can you direct me to that topic? Thanks a lot! Alex