NAME
protonate - protonates structures
VERSION 4.0.1
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
-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
-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
gromacs(7)
More information about GROMACS is available at
<http://www.gromacs.org/>.
Thu 16 Oct 2008 protonate(1)