Hi Sanku,
you can use APBS (Adaptive Poisson-Boltzman Solver,
http://www.poissonboltzmann.org/apbs/ ).
This program computes the PB equation on a single conformation, but you
can write a script to calculate values over trajectory.
APBS has the advances to be integrated into VMD and pymol, moreover is
avalaible an MPI parallelized version.
Francesco
Il 17/07/2011 02:47, Mark Abraham ha scritto:
On 17/07/2011 10:45 AM, Justin A. Lemkul wrote:
Sanku M wrote:
I thought since the implicit solvent model has been invoked
recently, there might be some features for PB calculation as well.
You can get GB polarization energies with the implicit solvent code,
but not PB, as far as I am aware. If there are undocumented
features, perhaps one of the developers can comment. But given the
lack of any documentation on the matter, I would conclude that direct
PB calculations cannot be done at present.
They can't
Mark
-Justin
------------------------------------------------------------------------
*From:* Justin A. Lemkul <jalem...@vt.edu>
*To:* Discussion list for GROMACS users <gmx-users@gromacs.org>
*Sent:* Sat, July 16, 2011 7:35:43 PM
*Subject:* Re: [gmx-users] Poisson-Boltzmann free energy in gromacs?
Sanku M wrote:
> Hi,
> I was wondering whether, in gromacs, there is any way of
calculating the electrostatic free energy using poisson Boltzmann
equation.
There is no mention of such a feature in the manual, so I would
suspect the answer is no.
-Justin
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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