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gmx-protonate(1)                GROMACS Manual                gmx-protonate(1)

NAME
       gmx-protonate - Protonate structures

SYNOPSIS
       gmx protonate [-s [<.tpr/.tpb/...>]] [-f [<.xtc/.trr/...>]]
                    [-n [<.ndx>]] [-o [<.xtc/.trr/...>]] [-nice <int>]
                    [-b <time>] [-e <time>] [-dt <time>]

DESCRIPTION
       gmx protonate reads (a) conformation(s) and adds all missing hydrogens
       as defined in oplsaa.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.

OPTIONS
       Options to specify input and output files:

       -s [<.tpr/.tpb/...>] (topol.tpr) (Input)
           Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent

       -f [<.xtc/.trr/...>] (traj.xtc) (Input, Optional)
           Trajectory: xtc trr cpt trj gro g96 pdb tng

       -n [<.ndx>] (index.ndx) (Input, Optional)
           Index file

       -o [<.xtc/.trr/...>] (protonated.xtc) (Output)
           Trajectory: xtc trr trj gro g96 pdb tng

       Other options:

       -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 ISSUES
       - 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/>.

VERSION 5.0.6                                                 gmx-protonate(1)