g_protonate(1) [debian man page]

g_protonate(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				    g_protonate(1)

NAME

       g_protonate - protonates structures

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_protonate -s topol.tpr -f traj.xtc -n index.ndx -o protonated.xtc -[no]h -[no]version -nice int -b time -e time -dt time

DESCRIPTION

	g_protonate reads (a) conformation(s) and adds all missing hydrogens as defined in  gmx2.ff/aminoacids.hdb. If only  -s is specified, this
       conformation will be protonated, if also  -f is specified, the conformation(s) will be read from this file, which can be  either  a  single
       conformation or a trajectory.

       If  a   .pdb  file  is supplied, residue names might not correspond to to the GROMACS naming conventions, in which case these residues will
       probably not be properly protonated.

       If an index file is specified, please note that the atom numbers should correspond to the  protonated state.

FILES

       -s topol.tpr Input
	Structure+mass(db): tpr tpb tpa gro g96 pdb

       -f traj.xtc Input, Opt.
	Trajectory: xtc trr trj gro g96 pdb cpt

       -n index.ndx Input, Opt.
	Index file

       -o protonated.xtc Output
	Trajectory: xtc trr trj gro g96 pdb

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	Print version info and quit

       -nice int 0
	Set the nicelevel

       -b time 0
	First frame (ps) to read from trajectory

       -e time 0
	Last frame (ps) to read from trajectory

       -dt time 0
	Only use frame when t MOD dt = first time (ps)

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011						    g_protonate(1)

g_dih(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c					  g_dih(1)

NAME

       g_dih - analyzes dihedral transitions

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_dih -f traj.xtc -s topol.tpr -o hello.out -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -[no]sa -mult int

DESCRIPTION

	g_dih can do two things. The default is to analyze dihedral transitions by merely computing all the dihedral angles defined in your topol-
       ogy for the whole trajectory. When a dihedral flips over to another minimum an angle/time plot is made.

       The opther option is to discretize the dihedral space into a number of bins, and group each conformation in dihedral space in the appropri-
       ate bin. The output is then given as a number of dihedral conformations sorted according to occupancy.

FILES

       -f traj.xtc Input
	Trajectory: xtc trr trj gro g96 pdb cpt

       -s topol.tpr Input
	Run input file: tpr tpb tpa

       -o hello.out Output
	Generic output file

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	Print version info and quit

       -nice int 19
	Set the nicelevel

       -b time 0
	First frame (ps) to read from trajectory

       -e time 0
	Last frame (ps) to read from trajectory

       -dt time 0
	Only use frame when t MOD dt = first time (ps)

       -[no]wno
	View output  .xvg,  .xpm,  .eps and  .pdb files

       -[no]sano
	Perform cluster analysis in dihedral space instead of analysing dihedral transitions.

       -mult int -1
	mulitiplicity for dihedral angles (by default read from topology)

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011							  g_dih(1)