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NAME

       g_protonate - protonates structures

       VERSION 4.6.6

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 7 Jul 2014                  g_protonate(1)



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