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Re: WSN: free energies calculations (fwd)
Sender: Rafael Iosef Najmanovich Szeinfeld <szeinfel@snfma1.if.usp.br>
Subject: Re: WSN: free energies calculations
Hi Netters
Pieter Stouten Asked me to be more precise in order to get more
useful help. I'll tell you what exactly I want and perhaps someone may
help me.
I'm doing some montecarlo simulations on the HP protein folding
model of Ken Dill. Until the moment I'm just writing a program that
reproduces his model.
The HP model (as most of the models) Hamiltonian is a sumation
only on hydrophobic contacts (a good approximation since the hydrophobic
effect is the diving force to fold a protein). I'd like to see what
happens if we assign an energy to the polar contacts and to the
hydrophobic-polar contact, but the magnitude of this contacts must resemble
to some extend what happens in real proteins.
So I'd like to know, on your point of view, if we assing a unity
of energy to the hydrophobic contact (H-H), what would be the energy of a
polar contact (P-P) and hydrophobic-polar (H-P) ?
Sincerly yours,
Rafael.
*---------------------------------------------------------------------------*
*Rafael Iosef Najmanovich Szeinfeld |SMAIL: Depto. de Bioquimica - B10 INF*
*Dept. Biochemistry -Chemistry Inst. | Universidade de Sao Paulo *
*Dept. Math. Physics -Physics Inst. | Av. Prof. Lineu Prestes 748 *
*University of Sao Paulo | CEP 05508-900 *
*E-MAIL : szeinfel@snfma1.if.usp.br | Sao Paulo - SP - Brazil *
*---------------------------------------------------------------------------*