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       g_confrms - fits two structures and calculates the rmsd

       VERSION 4.0.1


       g_confrms  -f1  conf1.gro  -f2  conf2.gro  -o  fit.pdb -n1 fit1.ndx -n2
       fit2.ndx  -no  match.ndx  -[no]h  -nice  int  -[no]w  -[no]one  -[no]mw
       -[no]pbc -[no]fit -[no]name -[no]label -[no]bfac


       g_confrms  computes  the  root  mean  square  deviation  (RMSD)  of two
       structures after LSQ fitting the second structure  on  the  first  one.
       The  two  structures do NOT need to have the same number of atoms, only
       the two index groups used for the  fit  need  to  be  identical.   With
       -name  only  matching  atom names from the selected groups will be used
       for the fit and RMSD calculation. This can  be  useful  when  comparing
       mutants of a protein.

       The  superimposed  structures  are written to file. In a  .pdb file the
       two  structures  will  be  written  as  separate  models  (use   rasmol
       -nmrpdb).  Also  in  a  .pdb file, B-factors calculated from the atomic
       MSD values can be written with  -bfac.


       -f1 conf1.gro Input
        Structure+mass(db): tpr tpb tpa gro g96 pdb

       -f2 conf2.gro Input
        Structure file: gro g96 pdb tpr tpb tpa

       -o fit.pdb Output
        Structure file: gro g96 pdb

       -n1 fit1.ndx Input, Opt.
        Index file

       -n2 fit2.ndx Input, Opt.
        Index file

       -no match.ndx Output, Opt.
        Index file


        Print help info and quit

       -nice int 19
        Set the nicelevel

        View output xvg, xpm, eps and pdb files

        Only write the fitted structure to file

        Mass-weighted fitting and RMSD

        Try to make molecules whole again

        Do  least  squares  superposition  of  the  target  structure  to  the

        Only compare matching atom names

        Added chain labels A for first and B for second structure

        Output B-factors from atomic MSD values



       More      information     about     GROMACS     is     available     at

                                Thu 16 Oct 2008                   g_confrms(1)