Thank you Justin for your prompt reply, as usual :)
With the last 2 lines of my previous post, I was referring on how to build *.itp files for completely new molecules (say lipids such as DMPC, DMPE or glutathione) that are not defined in the forcefield. I.e. how to derive dihedral angle code, force constant, etc. so that this new molecules could be used in the simulation. I.e. how to build your own *.itp and *.top files. Or better said, how the parameters for already defined molecules in the forcefield, such as amino-acids and ions were created? Where can we get more information about this ins and outs of building your own topologies? Maybe there are some good references that you can refer me?
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