[gmx-users] Forcefield parameters for Zinc

[Emma A]

> > Hi,
> > Related to the Zn-parameters; where can I find the reference (author,
> > journal, year) to the sigma and epsilon (1.95998e-01  5.23000e-02)
> > parameters that I find in /gromacs/top/amber99sb.ff/ffnonbonded.itp for 
[
> > atomtypes ] Zn.
> >
> > I would like to use amber99sb force field in my Gromacs simulation of a 
Zn-
> > containing protein.
> >
> > Best regards,
> > Emma
> >
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> > Emma Ahlstrand
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Leandro Bortot <leandro.obt at ...> writes:

> 
> Hi Emma,
> 
>      Just sharing some experience here: I tried to use the AMBER99SB-ILDN
> forcefield, which has the same Zn parameter as AMBER99SB, for simulating a
> Zn-binding protein and it was actually not possible to study the Zn-
binding
> process.
>      This happens essentially because it is not a good approximation to
> consider Zn2+ as a charged sphere and expect it to bind strongly to CysH,
> or even Cys-, and to His during the simulations because these are not
> simple charge-charge interactions.
> 
>      Some approaches for better results are to use a tetrahedral model for
> zinc (Cationic Dummy Atom Approach), use His-Zn and Cys-Zn bonding
> parameters or to perform QM/MM.
>      I don't know about the tetrahedral model, but using bonding 
parameters
> will certainly ensure the bonded state. I believe you can find such
> parameters for AMBER99SB in the literature.
> 
> I hope it helps,
> Leandro.

Hi Leandro,
thanks for your reply.
I did not expect the parameters for Zn in Amber99sb to work directly (I was 
thinking of adding distance restraints on Zn-His interaction). However in a 
short equilibration the parameters did work and the Zn stayed in the protein 
as it should. So I would like to know more about the work behind these LJ 
sigma and epsilon parameters and how the were chosen and evaluated. 

Does anyone know where I find the reference to the LJ sigma and epsilon 
parameters that I find in /gromacs/top/amber99sb.ff/ffnonbonded.itp for 
[atomtypes ] Zn?

Best regards,
Emma