[gmx-users] Re:Ka/Kd

[Justin Lemkul]

On 11/5/12 9:59 AM, lloyd riggs wrote:
> Quick question,
>
> I went and calculated the Ka/Kd with the g_hbond --> -g_analyze and just wondered, if all my simulations are pulled, does it in the end make any sense, or is there ways to compensate for this.  I assume the h_bond life would be meaningless, as under a normal situation, 2 proteins h-bond lifes could stretch into the seconds (minus fluctuation around a very small bound area)...
>

Extracting equilibrium properties from a non-equilibrium simulation is dicey, 
indeed.  I've never attempted such a thing myself, but I would think determining 
Kd from deltaG would be more reliable, at least inasmuch as the deltaG estimate 
is reliable (i.e., from umbrella sampling and a proper assessment of errors).

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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