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protonate
Langue: en
Version: 262121 (debian - 07/07/09)
Section: 1 (Commandes utilisateur)
NAME
protonate - protonates structuresSYNOPSIS
protonate -s topol.tpr -f traj.xtc -n index.ndx -o protonated.xtc -[no]h -nice int -b time -e time -dt timeDESCRIPTION
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 InputStructure+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 noPrint 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 the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.
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