1GMX-CONFRMS(1)                      GROMACS                     GMX-CONFRMS(1)
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NAME

6       gmx-confrms - Fit two structures and calculates the RMSD
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SYNOPSIS

9          gmx confrms [-f1 [<.tpr/.gro/...>]] [-f2 [<.gro/.g96/...>]]
10                      [-n1 [<.ndx>]] [-n2 [<.ndx>]] [-o [<.gro/.g96/...>]]
11                      [-no [<.ndx>]] [-[no]w] [-[no]one] [-[no]mw] [-[no]pbc]
12                      [-[no]fit] [-[no]name] [-[no]label] [-[no]bfac]
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DESCRIPTION

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

29       Options to specify input files:
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31       -f1 [<.tpr/.gro/…>] (conf1.gro)
32              Structure+mass(db): tpr gro g96 pdb brk ent
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34       -f2 [<.gro/.g96/…>] (conf2.gro)
35              Structure file: gro g96 pdb brk ent esp tpr
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37       -n1 [<.ndx>] (fit1.ndx) (Optional)
38              Index file
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40       -n2 [<.ndx>] (fit2.ndx) (Optional)
41              Index file
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43       Options to specify output files:
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45       -o [<.gro/.g96/…>] (fit.pdb)
46              Structure file: gro g96 pdb brk ent esp
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48       -no [<.ndx>] (match.ndx) (Optional)
49              Index file
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51       Other options:
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53       -[no]w (no)
54              View output .xvg, .xpm, .eps and .pdb files
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56       -[no]one (no)
57              Only write the fitted structure to file
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59       -[no]mw (yes)
60              Mass-weighted fitting and RMSD
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62       -[no]pbc (no)
63              Try to make molecules whole again
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65       -[no]fit (yes)
66              Do least squares superposition of the target  structure  to  the
67              reference
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69       -[no]name (no)
70              Only compare matching atom names
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72       -[no]label (no)
73              Added chain labels A for first and B for second structure
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75       -[no]bfac (no)
76              Output B-factors from atomic MSD values
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SEE ALSO

79       gmx(1)
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81       More     information    about    GROMACS    is    available    at    <‐
82       http://www.gromacs.org/>.
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85       2020, GROMACS development team
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902019.6                           Feb 28, 2020                   GMX-CONFRMS(1)
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