Main Table of Contents

Fri 5 Jul 2013


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 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.


-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]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-[no]one bool no Only write the fitted structure to file
-[no]mw bool yes Mass-weighted fitting and RMSD
-[no]pbc bool no Try to make molecules whole again
-[no]fit bool yes Do least squares superposition of the target structure to the reference
-[no]name bool no Only compare matching atom names
-[no]label bool no Added chain labels A for first and B for second structure
-[no]bfac bool no Output B-factors from atomic MSD values