gmx-protonate(1) GROMACS Manual gmx-protonate(1)NAMEgmx-protonate - Protonate structures
SYNOPSIS
gmx protonate [-s [<.tpr/.tpb/...>]] [-f [<.xtc/.trr/...>]]
[-n [<.ndx>]] [-o [<.xtc/.trr/...>]] [-nice <int>]
[-b <time>] [-e <time>] [-dt <time>]
DESCRIPTION
gmx protonate reads (a) conformation(s) and adds all missing hydrogens
as defined in oplsaa.ff/aminoacids.hdb. If only -s is specified, this
conformation will be protonated, if also -f is specified, the conforma‐
tion(s) will be read from this file, which can be either a single con‐
formation 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 prob‐
ably not be properly protonated.
If an index file is specified, please note that the atom numbers should
correspond to the protonated state.
OPTIONS
Options to specify input and output files:
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent
-f [<.xtc/.trr/...>] (traj.xtc) (Input, Optional)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-n [<.ndx>] (index.ndx) (Input, Optional)
Index file
-o [<.xtc/.trr/...>] (protonated.xtc) (Output)
Trajectory: xtc trr trj gro g96 pdb tng
Other options:
-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)
KNOWN ISSUES
- For the moment, only .pdb files are accepted to the -s flag
SEE ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-protonate(1)
