Poisson Boltzmann with NAMD

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Wed Sep 06 2006 - 19:47:49 CDT

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 Interlandi gianluca_at_u.washington.edu
                    +1 (206) 685 4435
                    +1 (206) 714 4303

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.

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