1 .TH protonate 1 "Thu 16 Oct 2008"
3 protonate - protonates structures
10 .BI "-n" " index.ndx "
11 .BI "-o" " protonated.xtc "
20 reads (a) conformation(s) and adds all missing
21 hydrogens as defined in
26 specified, this conformation will be protonated, if also
29 is specified, the conformation(s) will be read from this file
30 which can be either a single conformation or a trajectory.
34 If a pdb file is supplied, residue names might not correspond to
35 to the GROMACS naming conventions, in which case these residues will
36 probably not be properly protonated.
40 If an index file is specified, please note that the atom numbers
41 should correspond to the
47 Structure+mass(db): tpr tpb tpa gro g96 pdb
51 Trajectory: xtc trr trj gro g96 pdb cpt
57 .BI "-o" " protonated.xtc"
59 Trajectory: xtc trr trj gro g96 pdb
63 Print help info and quit
65 .BI "-nice" " int" " 0"
68 .BI "-b" " time" " 0 "
69 First frame (ps) to read from trajectory
71 .BI "-e" " time" " 0 "
72 Last frame (ps) to read from trajectory
74 .BI "-dt" " time" " 0 "
75 Only use frame when t MOD dt = first time (ps)