If there is a GL dipeptide, how can I calculate no. of non bonded or excluded atoms?
I am not sure what you are looking for here. A dipeptide with sequence GL is made of the two amino acids glycine and leucine which are bond together with an amid bond.
Your question needs to be clearer. I think, you need to mention the atoms in the GL dipeptide. For example, the two H atoms of amino terminus in GL are non-bonded to the H atom of the peptide (or amide) bond. Likewise, the two H atoms of C-alpha of 'Glycine' in GL are non-bonded to the H atom of the peptide (or amide) bond. And one can extend this further by considering all the atoms in the dipeptide GL. I hope, this explanation is understandable.
Mr. Kristiansen,
i am using amber for getting the topology file. in the attached document, i have used two residues for this example. so after getting topology file (.prmtop), no of excluded atoms as calculated by the software is 148. i think this is what i am not understanding.
thank you
Mr. Sabareesh,
i have attached a photo of atoms. so finally after calculation, no of excluded atoms is 148. could you explain this?
thank you
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