I am new to this forum. I am also new to molecular dynamics modeling, I don't even know how to begin to solve my problem. I have the protein database (pdb) file for ONE diphenylalanine FF peptide (C15H15NO2). What I want to do is to turn this monomer into a dimer by "attaching" another diphenylalanine monomer to the first monomer, making it a diphenylalanine FF DIMER. (Diphenylalanine has a tendency to self-assemble into nanrods or nanotubes, and that is what I want to show.) But HOW do I do this on VMD? In the VMD Main window, you can go to the Extensions plugin, and then you can see Modeling in the drop-down menu and from here you can choose Molefacture. But where I am lost is what you have to do once you are in the Molefacture--Molecules Builder window. As I mentioned, I have the pdb file for one diphenylalanine molecule and I want to model TWO of these molecules in a waterbox given this file. Where exactly does the second molecule attach itself to the first? Let's say I want to attach the second molecule to the charged termini (or terminus) of the first molecule. Where IS the charged termini of diphenylalanine? Is it the NH2? Is it one of the H atoms in one of the phenyl rings? Where do the two molecules join? And HOW do I do this in molefacture? I don't know much about biology/chemistry/molecular modeling at all. Any help will be greatly appreciated.
