>> Can we analyse catalytic mechanism of an enzyme using the classical all >> atom MD simulation. > >No.
I would say, that is a bit too pessimistic and unnecessarily demotivating. You can not directly simulate the catalytic reaction without employing a quantum chemical treatment (or a reactive force field) for the catalytic site and the reacting compounds, but even without that, just with classical MD, you can still learn a lot about the enzymatic mechanism, e.g., about the binding of a substrate, the stabilization of reaction intermediates with respect to educt(s) and product(s) in the catalytic site relative to the same reaction in solution, the release of a product(s) etc. A literature research will turn up innumerable examples. -------------------------------------------------------------------------------------------------------------------------- R. Thomas Ullmann, PhD Theoretical & Computational Biophysics Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen, Germany thomas.ullm...@mpibpc.mpg.de www.bisb.uni-bayreuth.de/People/ullmannt -------------------------------------------------------------------------------------------------------------------------- ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Wednesday, September 03, 2014 1:42 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] All atom MD Simulation On 9/3/14, 7:40 AM, Anitha wrote: > Can we analyse catalytic mechanism of an enzyme using the classical all > atom MD simulation. > No. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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. -- 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.
