NAME

       gmx-confrms - Fit two structures and calculates the RMSD

SYNOPSIS

          gmx confrms [-f1 [<.tpr/.gro/...>]] [-f2 [<.gro/.g96/...>]]
                      [-n1 [<.ndx>]] [-n2 [<.ndx>]] [-o [<.gro/.g96/...>]]
                      [-no [<.ndx>]] [-[no]w] [-[no]one] [-[no]mw] [-[no]pbc]
                      [-[no]fit] [-[no]name] [-[no]label] [-[no]bfac]

DESCRIPTION

       gmx  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.

OPTIONS

       Options to specify input files:

       -f1 [<.tpr/.gro/...>] (conf1.gro)
              Structure+mass(db): tpr gro g96 pdb brk ent

       -f2 [<.gro/.g96/...>] (conf2.gro)
              Structure file: gro g96 pdb brk ent esp tpr

       -n1 [<.ndx>] (fit1.ndx) (Optional)
              Index file

       -n2 [<.ndx>] (fit2.ndx) (Optional)
              Index file

       Options to specify output files:

       -o [<.gro/.g96/...>] (fit.pdb)
              Structure file: gro g96 pdb brk ent esp

       -no [<.ndx>] (match.ndx) (Optional)
              Index file

       Other options:

       -[no]w (no)
              View output .xvg, .xpm, .eps and .pdb files

       -[no]one (no)
              Only write the fitted structure to file

       -[no]mw (yes)
              Mass-weighted fitting and RMSD

       -[no]pbc (no)
              Try to make molecules whole again

       -[no]fit (yes)
              Do least squares superposition of the target structure to the reference

       -[no]name (no)
              Only compare matching atom names

       -[no]label (no)
              Added chain labels A for first and B for second structure

       -[no]bfac (no)
              Output B-factors from atomic MSD values

SEE ALSO

       gmx(1)

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

COPYRIGHT

       2020, GROMACS development team