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)