g_confrms - fits two structures and calculates the rmsd
g_confrms -f1 conf1.gro -f2 conf2.gro -o fit.pdb -n1 fit1.ndx -n2
fit2.ndx -no match.ndx -[no]h -nice int -[no]w -[no]one -[no]mw
-[no]pbc -[no]fit -[no]name -[no]label -[no]bfac
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 tpb tpa
-o fit.pdb Output
Structure file: gro g96 pdb
-n1 fit1.ndx Input, Opt.
-n2 fit2.ndx Input, Opt.
-no match.ndx Output, Opt.
Print help info and quit
-nice int 19
Set the nicelevel
View output xvg, xpm, eps and pdb files
Only write the fitted structure to file
Mass-weighted fitting and RMSD
Try to make molecules whole again
Do least squares superposition of the target structure to the
Only compare matching atom names
Added chain labels A for first and B for second structure
Output B-factors from atomic MSD values
More information about GROMACS is available at
Thu 16 Oct 2008 g_confrms(1)