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Hope you're doing well. Actually I am working on a project related to DNA regulated Nanozyme and I have a nanozyme of mesoporous silica "Iron Manganese Silicate nanoparticle (IMSN) nanozyme". I have to do MD simulation of this inorganic particle with LAMMPS but for that I need its structure in PDB format for input files. I only know its chemical formula $\ce{FeMn(SiO4)}$ as I am new to inorganic nanoparticles simulations so I have to make this molecule in Avogadro. But I don't know how to generate this molecule like how this nanoparticle attaches in structure. Can anyone help me to build this molecule? or can anyone please guide me about its structure? Is this Silica act as a ligand or a core shell here? Your Answers are really appreciated. Thanks

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  • $\begingroup$ To keep things from getting too long here, I moved this discussion to chat $\endgroup$
    – Tyberius
    Aug 9 at 18:22
  • $\begingroup$ I know it's been awhile, but I think my original point still stands: building the structure per se isn't the problem, its that you don't know the structure. Determining what the structure even is seems to be a complicated research question in it's own right. $\endgroup$
    – Tyberius
    Nov 19 at 2:54