[gmx-users] how can i restrain Zn ion during simulations

Harry Mark Greenblatt harry.greenblatt at weizmann.ac.il
Mon Feb 19 10:36:32 CET 2018


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 M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology           harry.greenblatt at weizmann.ac.il<../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.&URL=mailto%3aharry.greenblatt%40weizmann.ac.il>
Weizmann Institute of Science        Phone:  972-8-934-6340
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