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


       g_confrms - fits two structures and calculates the rmsd VERSION 4.6.5


       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


         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.


       -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


        Print help info and quit

        Print version 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 reference

        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 <>.

                                          Mon 2 Dec 2013                             g_confrms(1)