Re: [gmx-users] how can i restrain Zn ion during simulations
BS”D I am currently running simulations for protein-RNA complex. However i have to include one Zn ion which is coordinated by 4 cysteine residues. when i performed energy minimization itself zinc displaces. How can i restrain to Zn, or to freeze Zn during simulations. You probably should use the ZAFF force field additions, from Ken Merz’s group. See Peters et al., J. Chem. Theory Comput. 2010, 6, 2935-2947. I have incorporated this into Gromacs amber99sb-ildn, for our work with Zn-fingers (but that was two His, two Cys coordination), and the Gromacs version of the newer Barcelona FF, with improved parameters for DNA and RNA (amber99bsc1). That system had four Cys residues binding Zn, like you have. If you want I can send you the ff files, assuming you want to use an Amber-based ff. Harry Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology harry.greenbl...@weizmann.ac.il<../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.=mailto%3aharry.greenblatt%40weizmann.ac.il> Weizmann Institute of SciencePhone: 972-8-934-6340 234 Herzl St.Facsimile: 972-8-934-3361 Rehovot, 7610001 Israel -- 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.
Re: [gmx-users] how can i restrain Zn ion during simulations
On 2/12/18 10:29 AM, vijayakumar gosu wrote: Dear gromacs users, I am currently running simulations for protein-RNA complex. However i have to include one Zn ion which is coordinated by 4 cysteine residues. when i performed energy minimization itself zinc displaces. How can i restrain to Zn, or to freeze Zn during simulations. Are you properly treating the Cys residues as anionic? If they're in the normal -SH state, I'd expect such a dissociation, but if they carry a -1 charge (as expected when coordinating Zn2+), I find that rather unusual. You can enforce the coordination geometry with bonds, harmonic connections, or distance restraints. Check the manual for explanations. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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.
[gmx-users] how can i restrain Zn ion during simulations
Dear gromacs users, I am currently running simulations for protein-RNA complex. However i have to include one Zn ion which is coordinated by 4 cysteine residues. when i performed energy minimization itself zinc displaces. How can i restrain to Zn, or to freeze Zn during simulations. Thanks in advance Best, Vijayakumar Gosu -- 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.
