NAME

       g_protonate - protonates structures

       VERSION 4.6.5

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)

KNOWN PROBLEMS

       - For the moment, only .pdb files are accepted to the -s flag

SEE ALSO

       gromacs(7)

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

                                          Mon 2 Dec 2013                           g_protonate(1)