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GMX-CONFRMS(1)			    GROMACS			GMX-CONFRMS(1)

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  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	files:

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

       -f2 [<.gro/.g96/^a|>] (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/^a|>] (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

2020.3				 Jul 09, 2020			GMX-CONFRMS(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT

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