[ESPResSo-users] protein self-aggregation, directional lennard jonnes

[sarah mohamadinegad]

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?

For example:

aa1   : N(type = 1) C(type = 2)

aa2   : N(type = 3) C(type = 4)

aa3   : 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,
Sarah