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

[raja]

Hi Tsjerk,

Thanks for your mails and for sharing valuable insight in current
discussion topic.

B.Nataraj



On Wed, 29 Nov 2006 14:28:17 +0100, "Tsjerk Wassenaar"
<tsjerkw at gmail.com> said:
> 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
> > > >
> > > > --
> > > > http://www.fastmail.fm - Access all of your messages and folders
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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
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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
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
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-- 
  raja
  raja_28 at fastmail.us

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