Section: GROMACS suite, VERSION 4.0.1 (1)Updated: Thu 16 Oct 2008Local indexUp
protonate - protonates structures
protonate-s topol.tpr -f traj.xtc -n index.ndx -o protonated.xtc -[no]h-nice int -b time -e time -dt time
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.