I'm trying to add a molecule in aminoacids.rtp (new user)

By looking at the pre defined amino acid entries and the chapter 5 of the manual I started building it up.  The fields that the file include for the [ atoms ] field are: 1. atom type, 2. "code name" taken from atomtypes.atp, 3. charge, 4. charge group.

My first question is: I know that in theory charge group is grouping atoms in order to get zero or an integer charge and that it has to be with as few atoms as possible. But aren't there any additional criteria for grouping atoms? I don't think that I have to make an arbitrary choice just for keeping an integer type of charge.

The second and most important question: the [ bonds ], [angles], [dihedrals], [improper] fields in the existing entries of aminoacids.rtp are defined only by atom type. I don't think I can use this format because an atom type is located in different location in my molecule, can be bonded with different atoms and has different charges. So I believe I have to use a type of numeration to define the proper bonding. With that in mind which is the proper syntax to do this in a proper way?

P.S.: I know that my questions are a bit obscure and hard to follow, sorry about that, not a native English speaker. Please feel free to ask me for any additional info necessary. Thanks in advance

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