[gmx-users] Forcefield parameters for Zinc

Mon Mar 16 14:53:09 CET 2015

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.

On Mon, Mar 16, 2015 at 9:59 AM, Emma A <emma.ahlstrand at lnu.se> wrote:

> Piggot T. <T.Piggot at ...> writes:
>
> >
> > Hi Mike,
> >
> > As well as the link that Bipin sent, you can also get parameters for
> GROMOS phosphorylated residues
> > (compatible with the 43A1 force field, I think) from:
> >
> > http://www.gromacs.org/Downloads/User_contributions/Force_fields
> >
> > I've never used either so have no idea which might be better. The ones
> that Binpin suggested look like they
> > work with the newer GROMOS 54A7 force field, so they might be the ones to
> use.
> >
> > On your other question, I am not sure about the protein-zinc parameters
> with a GROMOS force field. I would
> > say, is there any particular need for using one of the GROMOS protein
> force fields? There are definitely
> > parameters out there for some of the all-atom protein force fields (e.g.
> AMBER ones) which are probably
> > also better in terms of protein parameters.
> >
> > Cheers
> >
> > Tom
> >
> > PS: Hope things are good in the (relatively) new job!
> > ________________________________________
> > From: gromacs.org_gmx-users-bounces at ...
> > [gromacs.org_gmx-users-bounces at ...] on behalf
> > of Michael Carter [Michael.Carter at ...]
> > Sent: 20 August 2014 12:56
> > To: gmx-users at ...
> > Subject: Re: [gmx-users] Forcefield parameters for Zinc and
> phosphorylated
> residues
> >
> > Hi Bipin,
> >
> > Thanks for this. It works well for adding functionality to residues.
> >
> > Cheers,
> > Mike Carter
> >
> > On 20/08/2014 12:10, "bipin singh" <bipinelmat at ...> wrote:
> >
> > >This might help.
> > >
> > >http://vienna-ptm.univie.ac.at/
> > >
> > >
> > >
> > >*------------------------Thanks and Regards,Bipin Singh*
> > >
> > >
> > >
> > >On Wed, Aug 20, 2014 at 4:30 PM, Michael Carter <Michael.Carter at ...>
> > >wrote:
> > >
> > >> Hi,
> > >>
> > >> I have two questions regarding the parameterisation of Zinc ions and a
> > >> phosphorylated TYR residue within two different protein systems.
> > >>
> > >>
> > >>  1.  Zinc parameters:
> > >>
> > >> I have three zinc ions within one protein system. I want to use a
> bonded
> > >> model so that they do not fly out of my protein upon simulation. Is
> > >>there
> > >> any documentation on the parameters for such a model in the GROMOS
> > >> forcefield?
> > >>
> > >> 2. Phosphorylated TYR
> > >>
> > >> In another system I have a phosphorylated TYR residue. PDB2GMX does
> not
> > >> like this and after looking inot the manual I have found that you can
> > >>add
> > >> parameters for this to the existing forcefields. Much like the
> previous
> > >> question, is there any documentation on the addition of parameters for
> > >> phosphorylated residues in the GROMOS forcefield?
> > >>
> > >> Any pointers for these questions would be greatly appreciated.
> > >>
> > >> Cheers,
> > >> Mike Carter
> > >>
> > >> The Institute of Cancer Research: Royal Cancer Hospital, a charitable
> > >> Company Limited by Guarantee, Registered in England under Company No.
> > >> 534147 with its Registered Office at 123 Old Brompton Road, London SW7
> > >>3RP.
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>
> 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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