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

[Tristan Bereau]

Dear Sarah,

How you want to model a system ultimately depends on what you want to
recreate. However, atom types for protein backbones are generally
residue-independent, i.e., one set of parameters irrespective of the
residue. The interaction potential you refer to was used in this paper
to model CG peptides:

http://jcp.aip.org/resource/1/jcpsa6/v130/i23/p235106_s1

This model did use one atom type for the C atoms and another one for
the N atoms. See the following link for an ESPResSo implementation of
the CG model:

https://github.com/tbereau/peptideB

Best,
Tristan

On Sun, Feb 3, 2013 at 2:59 PM, sarah mohamadinegad <address@hidden> wrote:
> 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
>
>