.TH g_protonate 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_protonate - protonates structures

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_protonate\fP
.BI "\-s" " topol.tpr "
.BI "\-f" " traj.xtc "
.BI "\-n" " index.ndx "
.BI "\-o" " protonated.xtc "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.SH DESCRIPTION
\&\fB g_protonate\fR reads (a) conformation(s) and adds all missing
\&hydrogens as defined in \fB gmx2.ff/aminoacids.hdb\fR. If only \fB \-s\fR is
\&specified, this conformation will be protonated, if also \fB \-f\fR
\&is specified, the conformation(s) will be read from this file, 
\&which can be either a single conformation or a trajectory.
\&


\&If a \fB .pdb\fR 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 \fB protonated\fR state.
.SH FILES
.BI "\-s" " topol.tpr" 
.B Input
 Structure+mass(db): tpr tpb tpa gro g96 pdb 

.BI "\-f" " traj.xtc" 
.B Input, Opt.
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-o" " protonated.xtc" 
.B Output
 Trajectory: xtc trr trj gro g96 pdb 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 0" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.