From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Wed Sep 06 2006 - 20:34:49 CDT
Hi Gianluca,
Maybe you can try the program APBS (http://apbs.sourceforge.net/).
There is an interface between VMD and APBS to make the things easier.
Hope it helps!
Michel
2006/9/6, Gianluca Interlandi <gianluca_at_u.washington.edu>:
> Dear NAMD users,
>
> Is it possible to perform Poisson Boltzmann calculation with NAMD?
>
> I have simulated the wildtype and a single-point mutant of a protein. Both
> simulations were started from X-ray structures. It is experimentally known
> that the mutation stabilizes the structure. I want to know whether that
> mutation is electrostatically more favourable. Is a "Poisson Boltzmann
> calculation" the right approach? Would it be enough to calculate the
> interaction energy between the sidechain (in the WT and in the mutant) and
> the rest of the system to assert whether the mutated sidechain is
> energetically more favourable than the WT?
>
> Any hints would be appreciated.
>
> Gianluca
>
> -----------------------------------------------------
> Gianluca Interlandi gianluca_at_u.washington.edu
> +1 (206) 685 4435
> +1 (206) 714 4303
> http://biocroma.unizh.ch/gianluca/
>
> Postdoc at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:42:34 CST