table of contents
g_protonate(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_protonate(1) |
NAME¶
g_protonate - protonates structuresSYNOPSIS¶
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 timeDESCRIPTION¶
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.FILES¶
-s topol.tpr InputStructure+mass(db): tpr tpb tpa gro g96 pdb
Trajectory: xtc trr trj gro g96 pdb cpt
Index file
Trajectory: xtc trr trj gro g96 pdb
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame when t MOD dt = first time (ps)
SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |