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

[prasad]

Dear Gromacs Develpers and users,

Hoping a suggestion from any one of you for my problem.
I am simulating a system in vaccum force field (ffG43b1). In my protein
complex, I have a bare FE, which has
ligand bonds with NE2 of 4 HIS , OE1 and OE2 of one GLU.  Fe has 2+
originally.
Without iron my system has neutral charge. how can i take the charge of the
iron?
As IRON forms lignad bonds, does it has partial charge or it has its own
charge of Fe2+.
If it has the partial charge, i think i have to calculate the charges for
FE, GLU and HIS.
when it binds to the glutamic acid, is there any change in the charge of the
glutamic acid.

Since I am using the vaccum forcefield, all LYS and ARG has the neutral
charge. (All types of LYS, ARG, GLU, ASP are defined neutral in vaccum force
field).
How can i make the total system zero.
if i need to calculate the charges, which groups of residues should i
consider?
please give some suggestion.

Thank you very much in advance
prasad

> genion has the option of assigning a charge to a positive ion with -pq.
>You can also try making an itp file similar to ions.itp with your own
>definitions for ions.
i think genion replaces the solvent molecules. but in my system i am using
the vaccum forcefield.
in my system FE is not an individual ion. it has ligand bonds with glutamic
acid and histidine.
> grompp will give you a warning stating the overall charge of your system
if it is non-zero.  pdb2gmx produces a topology file that will tell you qtot
after each atom starting from atom 1.  Otherwise you can try looking at your
topology> file to see which residues are charged (most likely ARG, LYS for
positively> charged; ASP, GLU for negatively charged).  Your protein termini
may also
be> charged as well.
>
> genion has the option of assigning a charge to a positive ion with -pq.
You
> can also try making an itp file similar to ions.itp with your own
definitions for ions.
>
> grompp will give you a warning stating the overall charge of your system
if it> is non-zero.  pdb2gmx produces a topology file that will tell you
qtot
after> each atom starting from atom 1.  Otherwise you can try looking at
your
topology> file to see which residues are charged (most likely ARG, LYS for
positively> charged; ASP, GLU for negatively charged).  Your protein termini
may also
be> charged as well.> > total charge of my system should be neutral.
>> If you're positive (no pun intended!) that your system is correct, then
try> adding the necessary number of counterions (ie some Cl-) to your system
using> genion.