SYNOPSISg_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
DESCRIPTIONg_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.
FILES-f1 conf1.gro Input
Structure+mass(db): tpr tpb tpa gro g96 pdb
Structure file: gro g96 pdb tpr etc.
Structure file: gro g96 pdb etc.
Print help info and quit
Print version 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 reference
Only compare matching atom names
Added chain labels A for first and B for second structure
Output B-factors from atomic MSD values