[gmx-users] Re:Ka/Kd

[lloyd riggs]

Dear All,

Reguarding a question I asked below.  Does anyone know what the formulei, etc...are for g_sham taking in 2 columns (or 3 with time) and turning it into a density matrix.  Is it just a count, summation on x-y or other?

Stephan Watkins

-------- Original-Nachricht --------
> Datum: Thu, 08 Nov 2012 11:46:32 +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

> 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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