[gmx-users] Claculating Equilibrium constants

[Ran Friedman]

Hi Gideon,

If the binding is relatively weak and the force field parameters are good enough that should be feasible. See e.g., Biophys J. 2005 August; 89(2): 768–781.
However, in other cases this is more challenging. This is discussed in details for simulations of a Zinc binding protein in Phys Chem Chem Phys. 2009 Feb 14; 11(6): 975-83 

Good luck,
Ran

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Ran Friedman
Biträdande Lektor (Assistant Professor)

Linnaeus University
School of Natural Sciences
391 82 Kalmar, Sweden

+46 480 446 290 Telephone
+46 76 207 8763 Mobile
ran.friedman at lnu.se
http://lnu.se/research-groups/computational-chemistry-and-biochemistry-group?l=en
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From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of גדעון לפידות [glapidoth at gmail.com]
Sent: 30 November 2010 10:45
To: gmx-users at gromacs.org
Subject: [gmx-users] Claculating Equilibrium constants

Hello all,
I have a protein bound to ions. is there a way to calculate the Kd of the bound ion in Gromaces so I can compare it to experimental Kd?
Thanks,
Gideon