I am interested to study the interactions of synthetic polymers (formed by radical polymerizations) and their interactions with various types of nanoparticles/ligands. Unfortunaley I couldnt find any suitable sites or software where the optimized structure of that synthetic polymers can be obtained so that I can study their interactions with various small molecules. There are many database on protein structures only. Using Gaussian /Gaussview software (considering gross approximation ) very limited calculation can be done. It would be higly appreciated if you kindly suggest me any sites or softwares where I can study these computationally. Thanking you
Dear Abu Bin Imran, in fact, the computational study of the intermolecular interactions does not differ much from calculations of the small molecule ligand-protein interactions. Just there are some difficulties with calculations of your synthetic or (even natural) polymer's parameters because of some big data from them. You should take the smallest repeating unit of the macromolecule as much as possible and see what is the relationship between its interaction and structures with more repeating units (di-, tri-, and so on). You may use any of the following online and offline software for your inquiry: Autodock Tools, LigPrep, MOE, MAPS platform, DISI, Pipeline pilot, Hyperchem, etc.
Dear Abu Bin Imran, in fact, the computational study of the intermolecular interactions does not differ much from calculations of the small molecule ligand-protein interactions. Just there are some difficulties with calculations of your synthetic or (even natural) polymer's parameters because of some big data from them. You should take the smallest repeating unit of the macromolecule as much as possible and see what is the relationship between its interaction and structures with more repeating units (di-, tri-, and so on). You may use any of the following online and offline software for your inquiry: Autodock Tools, LigPrep, MOE, MAPS platform, DISI, Pipeline pilot, Hyperchem, etc.
Thank you so much Dr. Nodirali S. Normakhamatov for your nice explanation. It would be very much helpful.
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