1g_protonate(1)            GROMACS suite, VERSION 4.5            g_protonate(1)
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NAME

6       g_protonate - protonates structures
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8       VERSION 4.5
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SYNOPSIS

11       g_protonate  -s  topol.tpr  -f  traj.xtc -n index.ndx -o protonated.xtc
12       -[no]h -[no]version -nice int -b time -e time -dt time
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DESCRIPTION

15        protonate reads (a) conformation(s) and adds all missing hydrogens  as
16       defined  in   ffgmx2.hdb.  If  only  -s is specified, this conformation
17       will be protonated, if also  -f is specified, the conformation(s)  will
18       be  read  from this file which can be either a single conformation or a
19       trajectory.
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22       If a pdb file is supplied, residue names might not correspond to to the
23       GROMACS  naming conventions, in which case these residues will probably
24       not be properly protonated.
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27       If an index file is specified, please note that the atom numbers should
28       correspond to the  protonated state.
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FILES

31       -s topol.tpr Input
32        Structure+mass(db): tpr tpb tpa gro g96 pdb
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34       -f traj.xtc Input, Opt.
35        Trajectory: xtc trr trj gro g96 pdb cpt
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37       -n index.ndx Input, Opt.
38        Index file
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40       -o protonated.xtc Output
41        Trajectory: xtc trr trj gro g96 pdb
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OTHER OPTIONS

45       -[no]hno
46        Print help info and quit
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48       -[no]versionno
49        Print version info and quit
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51       -nice int 0
52        Set the nicelevel
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54       -b time 0
55        First frame (ps) to read from trajectory
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57       -e time 0
58        Last frame (ps) to read from trajectory
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60       -dt time 0
61        Only use frame when t MOD dt = first time (ps)
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SEE ALSO

65       gromacs(7)
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67       More   information  about  GROMACS  is  available  at  <http://www.gro‐
68       macs.org/>.
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72                                Thu 26 Aug 2010                 g_protonate(1)
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