Dear gmx-users: I read some research articles of calculating the binding free energy, still I can not figure out how to get the orientational parameters.
If I have the crystal structure of ligand bound protein, so I need to choose three anchor atoms in the protein and three anchor atoms in the ligand respectively? How to define these three atoms in ligand and protein, can I choose them arbitrarily? and then define one distance, two angles and three torsions? After I have the reference orientation, what should I do? Millions of thanks for answering my questions. Regards Chunxia -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
