Hi, There's no recipie to locate aggregation hot spots based on MD simulations. There are many papers on simulations of protein and peptide aggregation from which you can draw some ideas, but bear in mind that aggregation of more than very few and very small peptides is typically much slower than what one can simulate using atomistic MD.
For a quick approach you can use sequence analysis tools, e.g., TANGO http://tango.crg.es/ Good luck, Ran -- ------------------------------------------------------ Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355559 Email: [email protected] Skype: ran.friedman ------------------------------------------------------ shahid nayeem wrote: > Dear all > What are the analysis tools which should be used on MD trajectory file > in order to find potential aggregation sites of a protein. Anyone can > tell me about specific resource material on use of Gromacs to predict > protein aggregation hot spots from MD trajectory anlysis. > Shahid Nayeem -- gmx-users mailing list [email protected] http://lists.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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
