[gmx-users] Re:Ka/Kd

[lloyd riggs]

Thank you for the reply,

Figured.  Needless to say though, the software using the pulled gives about the same as by hand (although diffusion constants are also guessed but fit into what the computer calculates as compared on a scale of lysozyme,,yyyy, xxx, Fab fragments) but can not do the forward/backward (values of -65000.045/-74967.031), while the one way and integral give reasonable values, and the caculated (via g_hbond or g_hbond->g_analyze) DelG fits well also...

grüess

Stephan

-------- Original-Nachricht --------
> Datum: Mon, 05 Nov 2012 18:14:36 -0500
> Von: Justin Lemkul <jalemkul at vt.edu>
> An: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Betreff: Re: [gmx-users] Re:Ka/Kd

> 
> 
> 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
> 
> -- 
> ========================================
> 
> 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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