make_ndx(1) [debian man page]
make_ndx(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c make_ndx(1) NAME
make_ndx - makes index files VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
make_ndx -f conf.gro -n index.ndx -o index.ndx -[no]h -[no]version -nice int -natoms int DESCRIPTION
Index groups are necessary for almost every gromacs program. All these programs can generate default index groups. You ONLY have to use make_ndx when you need SPECIAL index groups. There is a default index group for the whole system, 9 default index groups for proteins, and a default index group is generated for every other residue name. When no index file is supplied, also make_ndx will generate the default groups. With the index editor you can select on atom, residue and chain names and numbers. When a run input file is supplied you can also select on atom type. You can use NOT, AND and OR, you can split groups into chains, residues or atoms. You can delete and rename groups. The atom numbering in the editor and the index file starts at 1. FILES
-f conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -n index.ndx Input, Opt., Mult. Index file -o index.ndx Output Index file OTHER OPTIONS
-[no]hno Print help info and quit -[no]versionno Print version info and quit -nice int 0 Set the nicelevel -natoms int 0 set number of atoms (default: read from coordinate or index file) SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 make_ndx(1)
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g_confrms(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_confrms(1) NAME
g_confrms - fits two structures and calculates the rmsd VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
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]bfac DESCRIPTION
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 com- paring mutants of a protein. The superimposed structures are written to file. In a .pdb file the two structures will be written as separate models (use rasmol -nmr- pdb). Also in a .pdb file, B-factors calculated from the atomic MSD values can be written with -bfac. FILES
-f1 conf1.gro Input Structure+mass(db): tpr tpb tpa gro g96 pdb -f2 conf2.gro Input Structure file: gro g96 pdb tpr etc. -o fit.pdb Output Structure file: gro g96 pdb etc. -n1 fit1.ndx Input, Opt. Index file -n2 fit2.ndx Input, Opt. Index file -no match.ndx Output, Opt. Index file OTHER OPTIONS
-[no]hno Print help info and quit -[no]versionno Print version info and quit -nice int 19 Set the nicelevel -[no]wno View output .xvg, .xpm, .eps and .pdb files -[no]oneno Only write the fitted structure to file -[no]mwyes Mass-weighted fitting and RMSD -[no]pbcno Try to make molecules whole again -[no]fityes Do least squares superposition of the target structure to the reference -[no]nameno Only compare matching atom names -[no]labelno Added chain labels A for first and B for second structure -[no]bfacno Output B-factors from atomic MSD values SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_confrms(1)