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Modeling Zinc ions
- Prunotto
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7 years 5 months ago #6066
by Prunotto
Modeling Zinc ions was created by Prunotto
Dear all,
since I would like to model a metalloprotein, I would need to model a Zinc ion: I realized that I cannot model these ions starting from the other MARTINI ions that are available (such as sodium, chlorine, calcium...) because these last ones were modelled to stay in solution, and as a matter of fact they also represent the first hydration shell (please correct me if I am wrong).
I already have in mind how I could model such an entity, but I have to ask you one fundamental (and perhaps trivial) question: is it possible to modify the Van der Waals radius of a MARTINI particle? I read in several of your papers that the VdW radius of a MARTINI bead is equal to 0.26 nm, however I cannot find this parameter into the .itp force field file...
Therefore, my question is: where is the VdW radius defined? Is it somehow hidden in the Lennard-Jones parameters? And is it possible to modify such radius?
I'm looking forward to hearing from you and I wish you a good day
Alessio
since I would like to model a metalloprotein, I would need to model a Zinc ion: I realized that I cannot model these ions starting from the other MARTINI ions that are available (such as sodium, chlorine, calcium...) because these last ones were modelled to stay in solution, and as a matter of fact they also represent the first hydration shell (please correct me if I am wrong).
I already have in mind how I could model such an entity, but I have to ask you one fundamental (and perhaps trivial) question: is it possible to modify the Van der Waals radius of a MARTINI particle? I read in several of your papers that the VdW radius of a MARTINI bead is equal to 0.26 nm, however I cannot find this parameter into the .itp force field file...
Therefore, my question is: where is the VdW radius defined? Is it somehow hidden in the Lennard-Jones parameters? And is it possible to modify such radius?
I'm looking forward to hearing from you and I wish you a good day
Alessio
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- peterkroon
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7 years 5 months ago #6076
by peterkroon
Replied by peterkroon on topic Modeling Zinc ions
Hi Alessio,
in principle you are correct that the Martini ions include the first solvation shell. However, since (atomistic) Zn is quite a bit bigger than, say, Na, you might be able to get away with it. Do note that the LJ interactions used in Martini (and the rest of MD) are isotropic, while d-orbitals are not.
The VdW radius is indeed defined by the LJ parameters. The usual Martini files specify combination rule 1 (defaults section), which means the LJ parameters (nonbond_params section) are described as a combination of C6 and C12. Consult the Gromacs manual for more details.
(Actually, the Martini parameters are given as a table of cross interaction between any two bead types, so extracting a radius for a single bead can be tricky. Is the radius of a particle even defined other than by its interactions with the rest of the world?)
If you have to add a new beadtype for your ion, you can look forward to a month of validating your new parameters. Can't you just take a Qa bead and accept that the size may be a bit off?
Also, reread the Martini 2007 paper (doi 10.1021/jp071097f); there's some information in there on what sigma was used.
Peter
in principle you are correct that the Martini ions include the first solvation shell. However, since (atomistic) Zn is quite a bit bigger than, say, Na, you might be able to get away with it. Do note that the LJ interactions used in Martini (and the rest of MD) are isotropic, while d-orbitals are not.
The VdW radius is indeed defined by the LJ parameters. The usual Martini files specify combination rule 1 (defaults section), which means the LJ parameters (nonbond_params section) are described as a combination of C6 and C12. Consult the Gromacs manual for more details.
(Actually, the Martini parameters are given as a table of cross interaction between any two bead types, so extracting a radius for a single bead can be tricky. Is the radius of a particle even defined other than by its interactions with the rest of the world?)
If you have to add a new beadtype for your ion, you can look forward to a month of validating your new parameters. Can't you just take a Qa bead and accept that the size may be a bit off?
Also, reread the Martini 2007 paper (doi 10.1021/jp071097f); there's some information in there on what sigma was used.
Peter
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- Pim
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7 years 5 months ago #6079
by Pim
Replied by Pim on topic Modeling Zinc ions
Yes, I don't think we ever considered zinc, but you can get some inspiration from our parametrization of chlorophylls and heme with coordinating Mg and Fe ions. You can find most info in
pubs.acs.org/doi/abs/10.1021/acs.jpcb.5b00809
and some updates in
pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b06865
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- siewert
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7 years 5 months ago #6095
by siewert
Replied by siewert on topic Modeling Zinc ions
Typically what we do in Martini when considering ions that have a structural role (e.g., in a protein or cofactor) is to constrain them to their position using some harmonic bonds to neighboring beads. This avoids (i) the ion from leaving the site, and (ii) steric clashes with the surrounding beads as non-bonded interactions are excluded between bonded beads.
For the size, if you fear the standard size (0.52 nm corresponds to the position of the well depth of the LJ potential for normal Martini beads) is too big, you can use a "S" type particle we also use for ring systems. So an SQa particle with a +2 charge would be a good choice for a Zn ion. Note, however, that the smaller size is only used in the interaction with other "S" type particles.
Another thing to potentially worry about is charge delocalization - some of the charge of the Zn ion might be spread over the neighboring atoms in reality. Only QM calculations can tell you to what extent this might be the case, but you could get an idea from looking at other all-atom force fields for similar proteins. See also the papers Pim referred to where we applied this trick in case of cofactors.
Good luck !
For the size, if you fear the standard size (0.52 nm corresponds to the position of the well depth of the LJ potential for normal Martini beads) is too big, you can use a "S" type particle we also use for ring systems. So an SQa particle with a +2 charge would be a good choice for a Zn ion. Note, however, that the smaller size is only used in the interaction with other "S" type particles.
Another thing to potentially worry about is charge delocalization - some of the charge of the Zn ion might be spread over the neighboring atoms in reality. Only QM calculations can tell you to what extent this might be the case, but you could get an idea from looking at other all-atom force fields for similar proteins. See also the papers Pim referred to where we applied this trick in case of cofactors.
Good luck !
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- Prunotto
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7 years 5 months ago #6113
by Prunotto
Replied by Prunotto on topic Modeling Zinc ions
Thank you very much to all of you for the very interesting answers!
My idea was in fact to model the non-bond interactions of the Zn ions with the surrounding residues through bond interactions. I was indeed going to ask whether S particles could be used in this case, or if problems may arise by using those. I will therefore try to use SQa particles in a first approximation and see if the results are acceptable.
Thank you again for your tips and hints!
All the best,
Alessio
My idea was in fact to model the non-bond interactions of the Zn ions with the surrounding residues through bond interactions. I was indeed going to ask whether S particles could be used in this case, or if problems may arise by using those. I will therefore try to use SQa particles in a first approximation and see if the results are acceptable.
Thank you again for your tips and hints!
All the best,
Alessio
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- prajwal07
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7 years 2 weeks ago #7208
by prajwal07
Replied by prajwal07 on topic Modeling Zinc ions
Hi Prunotto,
Have you generated parameters for Zn2+ ion in protein for CG MD simulation?
Would it be possible to share those with me.
Would it be possible to use those parameters for Mg2+ ion in protein for CG MD simulations?
Please let me know.
Have you generated parameters for Zn2+ ion in protein for CG MD simulation?
Would it be possible to share those with me.
Would it be possible to use those parameters for Mg2+ ion in protein for CG MD simulations?
Please let me know.
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- VH
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1 year 2 months ago #9572
by VH
Replied by VH on topic Modeling Zinc ions
Hi,
Have anybody of you generated parameters for Zn2+?
Is it possible to share them?
I would be grateful.
Have anybody of you generated parameters for Zn2+?
Is it possible to share them?
I would be grateful.
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