[gmx-users] ligand bond between iron and glutamic acid (vaccum force field)

[prasad]

Dear Tran,
thank you for giving answer to my mail.
> 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.

my question is if 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.

> 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.

since i am using the vaccum forcefield, all LYS and ARG has the neutral
charge. (All types of LYS, ARG, GLU, ASP are neutral).
How can i make the total system zero.

All residues have the neutral charge. FE has charge 2+.  Fe forms the ligand
bonds with the OE1 and OE2 of the one Glutamic acid and four HIS NE2.
when it binds to the glutamic acid, is there any change in the charge of the
glutamic acid.

please give some suggestion.




> >
> >         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?
>
> 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.
>
> > if i need to calculate the charges, which groups of residues should i
> consider?
>
> 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.