1 .TH g_protonate 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
3 g_protonate - protonates structures
5 .B VERSION 4.5.4-dev-20110404-bc5695c
8 .BI "\-s" " topol.tpr "
10 .BI "\-n" " index.ndx "
11 .BI "\-o" " protonated.xtc "
13 .BI "\-[no]version" ""
19 \&\fB g_protonate\fR reads (a) conformation(s) and adds all missing
20 \&hydrogens as defined in \fB gmx2.ff/aminoacids.hdb\fR. If only \fB \-s\fR is
21 \&specified, this conformation will be protonated, if also \fB \-f\fR
22 \&is specified, the conformation(s) will be read from this file,
23 \&which can be either a single conformation or a trajectory.
27 \&If a \fB .pdb\fR file is supplied, residue names might not correspond to
28 \&to the GROMACS naming conventions, in which case these residues will
29 \&probably not be properly protonated.
33 \&If an index file is specified, please note that the atom numbers
34 \&should correspond to the \fB protonated\fR state.
36 .BI "\-s" " topol.tpr"
38 Structure+mass(db): tpr tpb tpa gro g96 pdb
42 Trajectory: xtc trr trj gro g96 pdb cpt
44 .BI "\-n" " index.ndx"
48 .BI "\-o" " protonated.xtc"
50 Trajectory: xtc trr trj gro g96 pdb
54 Print help info and quit
56 .BI "\-[no]version" "no "
57 Print version info and quit
59 .BI "\-nice" " int" " 0"
62 .BI "\-b" " time" " 0 "
63 First frame (ps) to read from trajectory
65 .BI "\-e" " time" " 0 "
66 Last frame (ps) to read from trajectory
68 .BI "\-dt" " time" " 0 "
69 Only use frame when t MOD dt = first time (ps)
74 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.