table of contents
g_confrms(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_confrms(1) |
NAME¶
g_confrms - fits two structures and calculates the rmsdSYNOPSIS¶
g_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]bfacDESCRIPTION¶
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.FILES¶
-f1 conf1.gro InputStructure+mass(db): tpr tpb tpa gro g96 pdb
Structure file: gro g96 pdb tpr etc.
Structure file: gro g96 pdb etc.
Index file
Index file
Index file
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
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
SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |