Main Table of Contents

Thu 26 Aug 2010


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