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Platinum bead
- Rajat Desikan
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5 years 9 months ago #7694
by Rajat Desikan
Platinum bead was created by Rajat Desikan
Dear Martini experts,
I am looking at parameterizing organometallic molecules with platinum in it. Typically, the Pt atom forms 4 coordinate bonds with oxygen or nitrogen atoms around it. Can I get suggestions on how I can proceed with parameterization? Thank you for your time.
Warm regards,
Rajat
I am looking at parameterizing organometallic molecules with platinum in it. Typically, the Pt atom forms 4 coordinate bonds with oxygen or nitrogen atoms around it. Can I get suggestions on how I can proceed with parameterization? Thank you for your time.
Warm regards,
Rajat
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- riccardo
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5 years 9 months ago #7695
by riccardo
Replied by riccardo on topic Platinum bead
What do you need the model for? If it is for modeling a cofactor in a protein, you may find some inspiration in this publication:
D.H. de Jong, N. Liguori, T. van den Berg, C. Arnarez, X. Periole, S.J. Marrink. Atomistic and coarse grain topologies for the cofactors associated with the photosystem II core complex. JPCB, 119:7791–7803, 2015
Otherwise, note that metal-organic interactions are not in the realm of things which the Martini model is used for -- please see also this thread:
cgmartini.nl/index.php/component/kunena/...d-nanoparticle-au-np
D.H. de Jong, N. Liguori, T. van den Berg, C. Arnarez, X. Periole, S.J. Marrink. Atomistic and coarse grain topologies for the cofactors associated with the photosystem II core complex. JPCB, 119:7791–7803, 2015
Otherwise, note that metal-organic interactions are not in the realm of things which the Martini model is used for -- please see also this thread:
cgmartini.nl/index.php/component/kunena/...d-nanoparticle-au-np
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5 years 9 months ago #7696
by Rajat Desikan
Replied by Rajat Desikan on topic Platinum bead
Hi Riccardo,
Thank you for the quick reply. I plan to look at drug encapsulation within liposome nanoparticles. There are no proteins in my system at present.
I took a look at the paper above and saw that ions were modelled as charged particles (Q). I wonder if the same approach may work here as well. Your thoughts?
Regards,
Rajat
Thank you for the quick reply. I plan to look at drug encapsulation within liposome nanoparticles. There are no proteins in my system at present.
I took a look at the paper above and saw that ions were modelled as charged particles (Q). I wonder if the same approach may work here as well. Your thoughts?
Regards,
Rajat
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- riccardo
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5 years 9 months ago #7698
by riccardo
Replied by riccardo on topic Platinum bead
Let me rephrase my question. Where does the Pt come into play?
My point, which I also try to make in this older post ( cgmartini.nl/index.php/component/kunena/...d-nanoparticle-au-np ) is that if the metal that you want to describe is buried (for example, a gold nanoparticle which is functionalized with organic molecules, or a metal which is part of a heme group which is constrained on a pocket of a protein), the metal-organic interactions won't be critical. The interactions will be taking place between, say, the organic molecules on the surface of the metal nanoparticle and the environment. The metal-organic interactions are frozen to a certain configuration and, indeed, you may think to describe a metal center with a charge assuming that a metal in that particular environment is charged.
However, if your metal is "naked", and you want to be able to describe metal-organic interactions (you were talking about coordination shells of Pt) in a dynamic way, I do not think that Martini is the tool for that.
My point, which I also try to make in this older post ( cgmartini.nl/index.php/component/kunena/...d-nanoparticle-au-np ) is that if the metal that you want to describe is buried (for example, a gold nanoparticle which is functionalized with organic molecules, or a metal which is part of a heme group which is constrained on a pocket of a protein), the metal-organic interactions won't be critical. The interactions will be taking place between, say, the organic molecules on the surface of the metal nanoparticle and the environment. The metal-organic interactions are frozen to a certain configuration and, indeed, you may think to describe a metal center with a charge assuming that a metal in that particular environment is charged.
However, if your metal is "naked", and you want to be able to describe metal-organic interactions (you were talking about coordination shells of Pt) in a dynamic way, I do not think that Martini is the tool for that.
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5 years 9 months ago - 5 years 9 months ago #7699
by Rajat Desikan
Replied by Rajat Desikan on topic Platinum bead
Thank you for such a clear reply, Riccardo. I shall use a martinized version of my molecule for self-assembly and membrane insertion simulations where the hydrophobic organic moieties are important and not the metal.
I had another question. The atomic weight of Pt2+ is 195 and its vdw radius is 0.175 nm, which is very different from that of a Q particle. Any thoughts on how to proceed? I don't think that I can randomly change the attributes of a Q bead and expect Martini to behave normally.
Regards,
Rajat
I had another question. The atomic weight of Pt2+ is 195 and its vdw radius is 0.175 nm, which is very different from that of a Q particle. Any thoughts on how to proceed? I don't think that I can randomly change the attributes of a Q bead and expect Martini to behave normally.
Regards,
Rajat
Last edit: 5 years 9 months ago by Rajat Desikan.
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- riccardo
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5 years 9 months ago #7701
by riccardo
Replied by riccardo on topic Platinum bead
Definitely randomly changing the parameter of a Q bead won't lead you to a Pt bead, I agree :-) So, I don't have direct experience with that. I think you better first check the references you find at
www.cgmartini.nl/index.php/62-about/gallery/277-nano
like [Langmuir, 27:8323–8332, 2011], etc.. to see how people dealt with (gold) nanoparticles and the parametrization of the Au beads. Sorry but I can't be of more help for now.
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