g_confrms (1) - Linux Manuals

g_confrms: fits two structures and calculates the rmsd


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.
 Index file 

-n2 fit2.ndx Input, Opt.
 Index file 

-no match.ndx Output, Opt.
 Index file 


 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 reference

 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 <http://www.gromacs.org/>.