protonate(1)
NAME
protonate - protonates structures
SYNOPSIS
protonate -s topol.tpr -f traj.xtc -n index.ndx -o protonated.xtc -[no]h -nice int -b time -e time -dt time
DESCRIPTION
protonate reads (a) conformation(s) and adds all missing hydrogens as
defined in ffgmx2.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 xml
- -f traj.xtc Input, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
- -n index.ndx Input, Opt.
- Index file
- -o protonated.xtc Output
- Generic trajectory: xtc trr trj gro g96 pdb
OTHER OPTIONS
- -[no]h no
- Print help 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
- More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.