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

[raja]

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
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-- 
  raja
  raja_28 at fastmail.us

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