protonate(1) protonates structures


protonate -s topol.tpr -f traj.xtc -n index.ndx -o protonated.xtc -[no]h -nice int -b time -e time -dt time


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.


-s topol.tpr Input
 Structure+mass(db): tpr tpb tpa gro g96 pdb 

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

-n index.ndx Input, Opt.
 Index file 

-o protonated.xtc Output
 Trajectory: xtc trr trj gro g96 pdb 


 Print 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)