Provided by: gromacs-data_4.6.5-1build1_all bug

NAME
       g_confrms - fits two structures and calculates the rmsd VERSION 4.6.5


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


DESCRIPTION
        g_confrms computes the root mean square deviation (RMSD) of two structures after  least-squares  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.


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

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

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

       -n1 fit1.ndx Input, Opt.
        Index file

       -n2 fit2.ndx Input, Opt.
        Index file

       -no match.ndx Output, Opt.
        Index file


OTHER OPTIONS
       -[no]hno
        Print help info and quit

       -[no]versionno
        Print version info and quit

       -nice int 19
        Set the nicelevel

       -[no]wno
        View output  .xvg,  .xpm,  .eps and  .pdb files

       -[no]oneno
        Only write the fitted structure to file

       -[no]mwyes
        Mass-weighted fitting and RMSD

       -[no]pbcno
        Try to make molecules whole again

       -[no]fityes
        Do least squares superposition of the target structure to the reference

       -[no]nameno
        Only compare matching atom names

       -[no]labelno
        Added chain labels A for first and B for second structure

       -[no]bfacno
        Output B-factors from atomic MSD values


SEE ALSO
       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

                                                 Mon 2 Dec 2013                                     g_confrms(1)