Just as Mark and Justin have said, this is up to you to define this question.
The reason I said that, is you were asking "how do I know if my molecule is docked to the protein?". The first step to answering that question is defining what you mean by being docked. Once you have a definition, then you can look at your molecule / protein and see if it fulfills those requirements. I don't do docking, but from what I have seen is that what is of interest is how well something fits into a pocket, proximity to some groups, and interactions between the molecule and the protein (hydrogen bonding and hydrophobic). You really need to search the literature, as others will be doing something similar. And docking has been going on for a long time. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
