This is the message I originally posted in 2002: -------------------------------------------------------------- I have been looking again at the Lennard-Jones parameters (C6 and C12) I tried to derive from the MM3 force field epsilon and sigma values for manganese (Mn2+).
First of all, I compared the MM3-derived values for calcium (C6=1.014e-3 kJ.nm**6/mol; C12=4.579e-7 kJ.nm**12/mol) with the values defined in ffgmxnb.itp (C6=0.10052E-02; C12=0.49800E-06). The potential functions are plotted in red (MM3- derived) and green (ffgmxnb.itp). The curves are very similar. The minimum energy is slightly higher for the MM3-derived values. The blue curve is the potential for the values I calculated for manganese from the MM3 values (C6=5.848e-4; C12=6.631e-8). Next, I calculated the positions of the energy minima (sixth root of (2*C12)/C6): r_min (nm) calcium, ffgmxnb.itp 0.316 calcium, MM3-derived 0.311 manganese, MM3-derived 0.247 I then tried to compare this with published van der Waals and ionic radii, but so far this is very confusing. The ionic radius for Mn2+ in an octahedral coordination is 0.110 nm. The corresponding value for Ca2+ is 0.126 nm. Now I will check if the manganese binding site maintains the correct geometry during a dynamics run with these parameters. -------------------------------------------------------------- The stability of the coordination turned out to be OK. I never got round to my complete in-depth study of sugar binding by this metalloprotein, though :-) . -- Lieven Buts Department of Ultrastructure _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
