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g_confrmsMain Table of Contents |
VERSION 3.1
Thu 28 Feb 2002
| VERSION 3.1 |
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.
The superimposed structures are written to file. In a .pdb file the two structures will be written as separate models (use rasmol -nmrpdb).
| option | filename | type | description |
|---|---|---|---|
| -f1 | conf1.gro | Input | Structure+mass(db): tpr tpb tpa gro g96 pdb |
| -f2 | conf2.gro | Input | Generic structure: gro g96 pdb tpr tpb tpa |
| -o | fit.pdb | Output | Generic structure: gro g96 pdb |
| -n1 | fit1.ndx | Input, Opt. | Index file |
| -n2 | fit2.ndx | Input, Opt. | Index file |
| option | type | default | description |
|---|---|---|---|
| -[no]h | bool | no | Print help info and quit |
| -[no]X | bool | no | Use dialog box GUI to edit command line options |
| -nice | int | 19 | Set the nicelevel |
| -[no]one | bool | no | Only write the fitted structure to file |
| -[no]pbc | bool | no | Try to make molecules whole again |