Dear users and developers,
I am going to model a protein (almost large >200 aa) self-aggregation by using ESPResSo. To set hydrogen bond between amino acids of protein, I am going to use directional lennard jonnes (lj-angle).
As I should consider hydrogen bond between N-H group of every amino acid with C-O group of other amino acids, do I have to assign different types to N and C groups of different amino acids?
aa1 : N(type = 1) C(type = 2)
aa2 : N(type = 3) C(type = 4)
N(type = 5) C(type = 6)
aa4 : N(type = 7) C(type = 8)
aa5 : N(type = 9) C(type = 10)
aa200: N(type = 399) C(type = 400)
I would be happy if I can assign only one type (for example 1) to all of my N atoms and another one (for example 2) to all my C atoms, Is it possible for the case of my problem?
Thanks in advance for your help,