Hi Gromacs Users, I'm running 20ns MD simulation of a protein kinase with ATP bond. I use amber99sb-ildn force field with parameters of ATP derived from the database of Richard Bryce.
What surprised me is that the ATP molecules displays a huge flexibility and conformational change. First, it slipped out from the starting binding pocket. In addition, the plane of adenine ring and ribose sugar rotate to about 180 degree after 10ns, making the ATP molecule looks weird. I never run a MD of a protein with ligand before. Is this something normal? What are possible causes for this? Maybe I should try some other ATP protein complex to see if the same thing happens? Thank you! Ruan -- 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.
