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

[Christopher Tran]

Quoting Prasad Gajula <prasad.gajula at uni-osnabrueck.de>:

> 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?

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.

> 
> i will be very much thankful to you.
> 
> 
> thnaks,
> prasad
> 
> 
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Christopher Tran
chr.tran at utoronto.ca