1 .TH g_confrms 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
3 g_confrms - fits two structures and calculates the rmsd
5 .B VERSION 4.5.4-dev-20110404-bc5695c
8 .BI "\-f1" " conf1.gro "
9 .BI "\-f2" " conf2.gro "
11 .BI "\-n1" " fit1.ndx "
12 .BI "\-n2" " fit2.ndx "
13 .BI "\-no" " match.ndx "
15 .BI "\-[no]version" ""
26 \&\fB g_confrms\fR computes the root mean square deviation (RMSD) of two
27 \&structures after least\-squares fitting the second structure on the first one.
28 \&The two structures do NOT need to have the same number of atoms,
29 \&only the two index groups used for the fit need to be identical.
30 \&With \fB \-name\fR only matching atom names from the selected groups
31 \&will be used for the fit and RMSD calculation. This can be useful
32 \&when comparing mutants of a protein.
36 \&The superimposed structures are written to file. In a \fB .pdb\fR file
37 \&the two structures will be written as separate models
38 \&(use \fB rasmol \-nmrpdb\fR). Also in a \fB .pdb\fR file, B\-factors
39 \&calculated from the atomic MSD values can be written with \fB \-bfac\fR.
41 .BI "\-f1" " conf1.gro"
43 Structure+mass(db): tpr tpb tpa gro g96 pdb
45 .BI "\-f2" " conf2.gro"
47 Structure file: gro g96 pdb tpr etc.
51 Structure file: gro g96 pdb etc.
53 .BI "\-n1" " fit1.ndx"
57 .BI "\-n2" " fit2.ndx"
61 .BI "\-no" " match.ndx"
67 Print help info and quit
69 .BI "\-[no]version" "no "
70 Print version info and quit
72 .BI "\-nice" " int" " 19"
76 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files
79 Only write the fitted structure to file
82 Mass\-weighted fitting and RMSD
85 Try to make molecules whole again
87 .BI "\-[no]fit" "yes "
88 Do least squares superposition of the target structure to the reference
90 .BI "\-[no]name" "no "
91 Only compare matching atom names
93 .BI "\-[no]label" "no "
94 Added chain labels A for first and B for second structure
96 .BI "\-[no]bfac" "no "
97 Output B\-factors from atomic MSD values
102 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.