Dear Justin, I had installed ambertools and followed the tutorial - http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm Currently, I am using gaussian to run the optimization part for obtaining parameters. During the process, I realized that the ligand is not picked up as a residue interacting with the metal ion (during the preparation of input files for gaussian).
My question is, is it advisable to convert the resultant files obtained from amber and convert it into cgenff compatible files using tools already available? Can I then switch over to GROMACS and use cgenff forcefield for running the simulation? Quoting your previous response - --------------------------------------------------------------------------- The CHARMM and GROMOS force fields support Fe2+ in the context of a heme residue. Anything else would not yet be parametrized. You are right that a divalent transition metal will inherently alter the properties of species around it (ligating residues, etc) but the only real solution for that is QM/MM if those behaviors are relevant to what you're interested in. If the Fe ion/atom is part of some larger cofactor, you'll either have to parametrize it (potentially arduous, given the limitations of additive force fields) or treat it quantum mechanically. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com On Mon, Dec 24, 2018 at 8:41 PM Prasanth G, Research Scholar < prasanthgha...@sssihl.edu.in> wrote: > Dear all, > > One of the proteins of my interest, has a FE2+ in the center and as it > plays a main role in the activity of the protein, it cannot be removed. > Can you please suggest a solution. I have tried with CHARMM and GROMOS, > with no success. > > > -- Regards, Prasanth. -- 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.