On 7/10/17 2:32 AM, 조영래 wrote:
Thank you Justin Every time your comment helped me. I should compare two system that are Zn_binding protein and Fe_binding protein. So I need force field that satisfies the following conditions. First, force field contains two metal ion (Fe and Zn)information. Second, force field contain metal ion binding mode amino acid information for example cysteine (CYM) in AMBER. However many force fields did not satisfied above conditions. So I would like to generate *.gro *itp file for metal atoms by GAMESS. But according to your comment this is not correct. In my case, the metal ions (Fe and Zn) binds one cysteine and two histidines. I want to simulate these complexes (i.e. Fe_protein and Zn_protein complex). Please suggest me an ideal force field that in able to be used for sumulation of the avode mentaioned complexes.
I don't know of one. Dealing with transition metals is one of the hardest tasks in parametrization. There's a reason why after many decades of development, the parameters still don't exist... Depending on what you need to do, hybrid QM/MM is probably the best/most straightforward approach. Classical force fields do not deal well with these kinds of systems.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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.
