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gmx-confrms(1)			GROMACS Manual			gmx-confrms(1)

NAME
       gmx-confrms - Fit two structures and calculates the RMSD

SYNOPSIS
       gmx confrms [-f1 [<.tpr/.tpb/...>]] [-f2 [<.gro/.g96/...>]]
		   [-o [<.gro/.g96/...>]] [-n1 [<.ndx>]] [-n2 [<.ndx>]]
		   [-no [<.ndx>]] [-nice <int>] [-[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  compar‐
       ing 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 and output files:

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

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

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

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

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

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

       Other options:

       -nice <int> (19)
	   Set the nicelevel

       -[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  ref‐
       erence

       -[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
       gromacs(7)

       More   information  about  GROMACS  is  available  at  <http://www.gro‐
       macs.org/>.

VERSION 5.0.6							gmx-confrms(1)

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