1g_confrms(1)              GROMACS suite, VERSION 4.5              g_confrms(1)
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NAME

6       g_confrms - fits two structures and calculates the rmsd
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8       VERSION 4.5
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SYNOPSIS

11       g_confrms  -f1  conf1.gro  -f2  conf2.gro  -o  fit.pdb -n1 fit1.ndx -n2
12       fit2.ndx -no match.ndx -[no]h -[no]version -nice  int  -[no]w  -[no]one
13       -[no]mw -[no]pbc -[no]fit -[no]name -[no]label -[no]bfac
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DESCRIPTION

16       g_confrms  computes the root mean square deviation (RMSD) of two struc‐
17       tures after LSQ fitting the second structure on the first one.  The two
18       structures  do  NOT need to have the same number of atoms, only the two
19       index groups used for the fit need to be identical.  With   -name  only
20       matching  atom  names from the selected groups will be used for the fit
21       and RMSD calculation. This can be useful when comparing  mutants  of  a
22       protein.
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25       The  superimposed  structures  are written to file. In a  .pdb file the
26       two structures will be written as separate models  (use   rasmol  -nmr‐
27       pdb).  Also  in  a  .pdb file, B-factors calculated from the atomic MSD
28       values can be written with  -bfac.
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FILES

31       -f1 conf1.gro Input
32        Structure+mass(db): tpr tpb tpa gro g96 pdb
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34       -f2 conf2.gro Input
35        Structure file: gro g96 pdb tpr etc.
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37       -o fit.pdb Output
38        Structure file: gro g96 pdb etc.
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40       -n1 fit1.ndx Input, Opt.
41        Index file
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43       -n2 fit2.ndx Input, Opt.
44        Index file
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46       -no match.ndx Output, Opt.
47        Index file
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OTHER OPTIONS

51       -[no]hno
52        Print help info and quit
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54       -[no]versionno
55        Print version info and quit
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57       -nice int 19
58        Set the nicelevel
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60       -[no]wno
61        View output xvg, xpm, eps and pdb files
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63       -[no]oneno
64        Only write the fitted structure to file
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66       -[no]mwyes
67        Mass-weighted fitting and RMSD
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69       -[no]pbcno
70        Try to make molecules whole again
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72       -[no]fityes
73        Do least squares superposition of the target structure to  the  refer‐
74       ence
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76       -[no]nameno
77        Only compare matching atom names
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79       -[no]labelno
80        Added chain labels A for first and B for second structure
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82       -[no]bfacno
83        Output B-factors from atomic MSD values
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SEE ALSO

87       gromacs(7)
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89       More   information  about  GROMACS  is  available  at  <http://www.gro‐
90       macs.org/>.
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94                                Thu 26 Aug 2010                   g_confrms(1)
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