Provided by: gromacs-data_2019.3-2_all bug

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

       2019, GROMACS development team