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-- Ray Luo, Ph.D. Professor of Structural Biology/Biochemistry/Biophysics, Chemical and Materials Physics, Chemical and Biomolecular Engineering, Biomedical Engineering, and Materials Science and Engineering Department of Molecular Biology and Biochemistry University of California, Irvine, CA 92697-3900 On Mon, Oct 26, 2020 at 9:31 PM SATYAJIT KHATUA <satyajitkhatua09.gmail.com> wrote: > > Dear Users, > > I am working on some ligand-bound metalloprotein systems. Following the > tutorials and manuals from ambermd site, I understood that system > preparation is a very important step here. Although there is a hint on how > MMPBSA.py can be used for the case of the ligand-protein complex in manual, > I am wondering how can I implement this into my systems as they contain a > catalytically important metal center at its active site (I think there is > no tutorial about the system preparation of a ligand-bound metalloprotein). > It is very straight forward in the case of the complex. For the ligand, it > is also not very hard to prepare the topologies. This leaves us only to the > parameterization of the protein system. Now as the metal center is > important, I can't just strip it off from the protein, right? And another > thing if there is any crystal water connected to that metal center to > fulfill its coordination number, should I have to retain it for the case of > protein parameterization (talking about protein only, not the complex)? > > with regards, > Satyajit Khatua > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Oct 30 2020 - 08:30:03 PDT