From: Juan José Galano Frutos (juanjogf_at_gmail.com)
Date: Mon Oct 07 2013 - 04:55:44 CDT
Hi dear all:
I would like to perform MD simulations to one protein which we already have
evaluated a series of kinetic and thermodynamic phi-values for a detailed
conformational folding/unfolding analysis (transition and intermediate
states included). In this sense, the literature suggest add a biasing
energy term leading the system to increasingly close conformations to those
suggested for the phi-values previously calculated.
Such biasing pseudoenergy term is definde as (an step function):
W(rho ,t)={[alpha * M(rho-rho0)˛]/2 if rho(t)> 0 , or 0 if
rho(t)<0} (Paci E, Vendruscolo M, Dobson CM, Karplus M (2002)
Determination of a transition state at atomic resolution from protein
engineering data. J Mol Biol 324:151–163)
where the parameter alpha controls the relative weight of the restraint
term with respect to the force field, and rho0 is equal to the lowest
value of the reaction coordinate reached by the system up to time t in the
simulation.
The reaction coordinate for the process, rho(t), is defined as the mean
square difference between the phi-value(sim) and the experimentally
determined phi-value(exp) values:
rho(t)= 1/N * sum[phi-value(sim) - phi-value(exp)˛] from 1 to N,
where N is the number of phi-value(exp) values used in the calculations.
Meanwhile, phi-value(sim) for one conformation C in the simulation is
defined as:
phi-value(sim) = ni(C)/ni(native), where ni(C) is defined as the number
of side-chain heavy atoms within a given cutoff distance. The ni(native)
term is the same but for the native conformation.
As you can see, I have clear what I would to do but I do not know is how in
NAMD. I have some programming skills and I made some scripts but I'm not an
expert in programming. I also researched and apparently this issue has
explicitly not been implemented yet in NAMD. If someone could suggest me
how to do it I would be happy.
Thanks very much in advance.
Juan José
Ph. D Student
Institute for Biocomputation and
Complex Systems Physics (BIFI)
Department of Biochemistry and
Molecular and Cellular Biology,
Sciences Faculty,
University of Zaragoza
Pedro Cerbuna # 12, 50009
Zaragoza
Spain
TEL: +34 976 76 28 06
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