[gmx-users] Inner product for two proteins eignevector trajectory

[Tsjerk Wassenaar]

Hi Raja,

Now the only reason that I did (briefly) read the paper you linked,
was because the subject interested me ;) Apparently, they did not
state which subset of Ca atoms they used. However, you can only make a
comparison like that if the sets of atoms included in the selection
are the same. Otherwise, you'd have a nice example of comparing apples
and oranges in a very improper manner. You might want to contact the
authors, or determine yourself which Ca atoms correspond between the
proteins. Now, to calculate the RMSIP, you need eigenvectors of equal
length, by definition. For such analysis to make sense, you also need
correspondence between the elements of the eigenvectors, i.e. the
atoms used for the analysis have to correspond.

Please note that the article shows that 2 ns is not enough for
simulations to have converged. You really want to do better than that
(and check the cosine content of the first pc's).

Cheers,

Tsjerk

On 11/29/06, raja <raja_28 at fastmail.us> wrote:
> Hi Tsjerk,
>
> Thanks for your reply. My purpose of calculating matrix of innerproduct
> is for calculation RMSIP (root mean square inner product) using a script
> (provided by you some month earlier). And I have found some references,
> showing comparison of RMSIP between more than two simulated systems
> consists of different proteins. How they could do it for whole protein?
> Since no indication of specific atoms selection in those reference
> pertaining to RMSIP calculation between the proteins.
>
> For example, this one reference which is readily available to download
>
>  "Native-state dynamics of the ubiquitin family: implications for
>  function and evolution"
>   J R Soc Interface. 2005 Mar 22;2(2):47-54
>
> http://www-jackson.ch.cam.ac.uk/Jackson_papers_files/2006_Marianayagam_Interface_UBQ.pdf
>
> I want to do similar analysis.
>
> Kindly reply me.
>
> B.Nataraj
>
>
>
>
> On Wed, 29 Nov 2006 11:30:00 +0100, "Tsjerk Wassenaar"
> <tsjerkw at gmail.com> said:
> > Hi Raja,
> >
> > Do the covariance analysis on a subset of your atoms, which is equal
> > in both structures, using index files.
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On 11/29/06, raja <raja_28 at fastmail.us> wrote:
> > > Hi gmxions,
> > > I like compute matrix of inner products using the command g_anaeig
> > > between eigenvector trr file of two different protein. When I do it, it
> > > shows error of dimension mismatch between two trr file, the error is
> > > understandable by me since eigen vectors computed for these two proteins
> > > are of different residue length, How to overcome this issue? Kindly
> > > reply me.
> > >
> > > With thanks!
> > > B.Nataraj
> > > --
> > >   raja
> > >   raja_28 at fastmail.us
> > >
> > > --
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> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > Junior UD (post-doc)
> > Biomolecular NMR, Bijvoet Center
> > Utrecht University
> > Padualaan 8
> > 3584 CH Utrecht
> > The Netherlands
> > P: +31-30-2539931
> > F: +31-30-2537623
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> --
>   raja
>   raja_28 at fastmail.us
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623