[gmx-users] Different sets of residues for ensemble fitting and RMSF calculation

[Xavier Periole]

Mark Berjanskii wrote:

>Dear all, 
>
>Is it possible to use different sets of residues for alignment of a
>protein ensemble and for calculation of RMSF?
>
>I am trying to get a plot RMSF vs residue number from a Gromacs 
>trajectory. I have an extended very flexible region in a protein of
>interest that I do not want to use for ensemble alignment because it
>will make RMSF of rigid secondary structure elements unreasonably big.
>
>
>Unfortunately, g_rmsf uses the same atom/residue selection for both
>ensemble alignment and calculation of RMSF. 
>
> Is it possible to somehow use only secondary structure regions of a
>protein for ensemble alignment but, then, calculate RMSF for each
>residue of the protein?
>  
>
That is indeed a bit anoying. I don't think it is possible !!
Perhaps make the fit using trjconv and turn off the fitting procedure in
the g_rmsf going directly in the code. There is a call for functions
    /* Remove periodic boundary */
    rm_pbc(&(top.idef),natom,box,x,x);

    /* Set center of mass to zero */
    sub_xcm(x,isize,index,top.atoms.atom,xcm,FALSE);
                                                                                                                              

    /* Fit to reference structure */
    do_fit(natom,w_rls,xref,x);

Check tcarefully that it is enought and recompile your g_rmsf !!
Perhaps it is enought.

It might be interesting that an option to fit and calculate the fluctuations
on different set of atoms is introduce in a next version of GROMACS.
This is not too much work !!!

XAvier

-- 
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   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   Nijenborgh 4
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: http://md.chem.rug.nl/~periole
   
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