Hi, I have a predicted secondary structure of a transmembrane protein containing a really long alpha helix. If I place the secondary structure of the protein inside membrane (as done for KALP in tutorial) and following all the steps perform a production MD, is it possible to obtain a thermodynamically favorable tertiary structure of the same protein ? I mean generating the folds based on the membrane environment provided.
Being a beginner in membrane protein simulation, any given advice will be highly appreciated. Thank you. -- Abhisek Mondal *Senior Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.