[gmx-users] Re:Ka/Kd

[lloyd riggs]

Dear All,

So I went over the below Ka/Kd...Seems doesnt fit for anything, the DelG I found doesnt change for components, and just fit my data for the first 20 analysis by chance I guess, except for Ent and Enth calculations from doing PCA, which break down nicely.  In case anyone reads this.

I have another couple questions regarding graphing.

-Regarding the output from g_gyrate, with the -nz option.  Is there a script somewhere to turn the x,y slices into a 3D plot or something (its around 40 slices for say an 8 Ang. Z , times each time point.  You can do it by hand, but that turns into plugging the numbers into a matrix by hand for 200 point per time frame....and most spread sheet things I have used (qti, Gnu, MS office) dont allow the manipulation of the data properly for such a plot, as its not simple cut and paste as with most plots.  In the end, one would most likely only need 2-3 snapshots over a run (200 points each) to show say a density of gyration for extreems, but you would have to look at most of them visually to find proper ones, especially from multiple runs)

-the same for ramachondran.  I basically want to just turn specific residues Vs. normal into histograms or a matrix with simple distribution (a 1 added to each 2D point for each occupancy to plot 3D ramachondrans).  This is not as bad as the gyrate, but still turns into 200 points per simulation, times 20 or so simulations.  I already know grace can take a column and turn it into a histogram, but not in 2D grids.  This I am sure is somewhere (a script or software), but have no clue whom/where to ask.

Sincerely,

Stephan Watkins

-------- Original-Nachricht --------
> Datum: Tue, 06 Nov 2012 13:18:48 +0100
> Von: "lloyd riggs" <lloyd.riggs at gmx.ch>
> An: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Betreff: Re: [gmx-users] Re:Ka/Kd

> 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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