gmx-sasa(1) GROMACS Manual gmx-sasa(1)NAMEgmx-sasa - Compute solvent accessible surface area
SYNOPSIS
gmx sasa [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]] [-n [<.ndx>]]
[-o [<.xvg>]] [-odg [<.xvg>]] [-or [<.xvg>]] [-oa [<.xvg>]]
[-tv [<.xvg>]] [-q [<.pdb>]] [-b <time>] [-e <time>]
[-dt <time>] [-tu <enum>] [-xvg <enum>] [-[no]rmpbc]
[-[no]pbc] [-sf <file>] [-selrpos <enum>] [-probe <real>]
[-ndots <int>] [-[no]prot] [-dgs <real>]
[-surface <selection>] [-output <selection>]
DESCRIPTION
gmx sasa computes solvent accessible surface areas. See Eisenhaber F,
Lijnzaad P, Argos P, Sander C, & Scharf M (1995) J. Comput. Chem. 16,
273-284 for the algorithm used. With -q, the Connolly surface can be
generated as well in a .pdb file where the nodes are represented as
atoms and the edges connecting the nearest nodes as CONECT records.
-odg allows for estimation of solvation free energies from per-atom
solvation energies per exposed surface area.
The program requires a selection for the surface calculation to be
specified with -surface. This should always consist of all non-solvent
atoms in the system. The area of this group is always calculated.
Optionally, -output can specify additional selections, which should be
subsets of the calculation group. The solvent-accessible areas for
these groups are also extracted from the full surface.
The average and standard deviation of the area over the trajectory can
be calculated per residue and atom (options -or and -oa).
With the -tv option the total volume and density of the molecule can be
computed. Please consider whether the normal probe radius is appropri‐
ate in this case or whether you would rather use, e.g., 0. It is good
to keep in mind that the results for volume and density are very
approximate. For example, in ice Ih, one can easily fit water molecules
in the pores which would yield a volume that is too low, and surface
area and density that are both too high.
OPTIONS
Options to specify input and output files:
-f [<.xtc/.trr/...>] (traj.xtc) (Input, Optional)
Input trajectory or single configuration: xtc trr cpt trj gro g96
pdb tng
-s [<.tpr/.tpb/...>] (topol.tpr) (Input, Optional)
Input structure: tpr tpb tpa gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Input, Optional)
Extra index groups
-o [<.xvg>] (area.xvg) (Output)
Total area as a function of time
-odg [<.xvg>] (dgsolv.xvg) (Output, Optional)
Estimated solvation free energy as a function of time
-or [<.xvg>] (resarea.xvg) (Output, Optional)
Average area per residue
-oa [<.xvg>] (atomarea.xvg) (Output, Optional)
Average area per atom
-tv [<.xvg>] (volume.xvg) (Output, Optional)
Total volume and density as a function of time
-q [<.pdb>] (connolly.pdb) (Output, Optional)
PDB file for Connolly surface
Other options:
-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 if t MOD dt == first time (ps)
-tu <enum> (ps)
Unit for time values: fs, ps, ns, us, ms, s
-xvg <enum> (xmgrace)
Plot formatting: none, xmgrace, xmgr
-[no]rmpbc (yes)
Make molecules whole for each frame
-[no]pbc (yes)
Use periodic boundary conditions for distance calculation
-sf <file>
Provide selections from files
-selrpos <enum> (atom)
Selection reference positions: atom, res_com, res_cog, mol_com,
mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog,
part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com,
dyn_res_cog, dyn_mol_com, dyn_mol_cog
-probe <real> (0.14)
Radius of the solvent probe (nm)
-ndots <int> (24)
Number of dots per sphere, more dots means more accuracy
-[no]prot (yes)
Output the protein to the Connolly .pdb file too
-dgs <real> (0)
Default value for solvation free energy per area (kJ/mol/nm2)
-surface <selection>
Surface calculation selection
-output <selection>
Output selection(s)SEE ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-sasa(1)
