debian man page for g_confrms

g_confrms(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				      g_confrms(1)

NAME
       g_confrms - fits two structures and calculates the rmsd

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS
       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

DESCRIPTION
	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  com-
       paring 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 -nmr-
       pdb). Also in a	.pdb file, B-factors calculated from the atomic MSD values can be written with	-bfac.

FILES
       -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

OTHER OPTIONS
       -[no]hno
	Print help info and quit

       -[no]versionno
	Print version info and quit

       -nice int 19
	Set the nicelevel

       -[no]wno
	View output  .xvg,  .xpm,  .eps and  .pdb files

       -[no]oneno
	Only write the fitted structure to file

       -[no]mwyes
	Mass-weighted fitting and RMSD

       -[no]pbcno
	Try to make molecules whole again

       -[no]fityes
	Do least squares superposition of the target structure to the reference

       -[no]nameno
	Only compare matching atom names

       -[no]labelno
	Added chain labels A for first and B for second structure

       -[no]bfacno
	Output B-factors from atomic MSD values

SEE ALSO
       gromacs(7)

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

								  Mon 4 Apr 2011						      g_confrms(1)