[gmx-users] ligand bond between iron and glutamic acid

[Prasad Gajula]

Dear gromacs users,

        i hope any of you give some suggestion for my problem.

i am simulating a system in vaccum force field. In my protein, Fe has
ligand bonds with NE2 of 4 histidines , OE1 and OE2 of GLU.  Without iron
my system has neutral charge. how can i take the charge of the iron? does
the charge effected by the partial charge of the GLU and HIS? if i need to
calculate the charges, which groups of residues should i consider?

total charge of my system should be neutral.

i will be very much thankful to you.


thnaks,
prasad