g_sas - computes solvent accessible surface area
g_sas -f traj.xtc -s topol.tpr -o area.xvg -or resarea.xvg -oa
atomarea.xvg -tv volume.xvg -q connelly.pdb -n index.ndx -i surfat.itp
-[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -probe real
-ndots int -qmax real -[no]f_index -minarea real -[no]pbc -[no]prot
g_sas computes hydrophobic, hydrophilic and total solvent accessible
surface area. As a side effect the Connolly surface can be generated
as well in a pdb file where the nodes are represented as atoms and the
vertices connecting the nearest nodes as CONECT records. The program
will ask for a group for the surface calculation and a group for the
output. The calculation group should always consists of all the
non-solvent atoms in the system. The output group can be the whole or
part of the calculation group. The area can be plotted per residue and
atom as well (options -or and -oa). In combination with the latter
option an itp file can be generated (option -i) which can be used to
restrain surface atoms.
By default, periodic boundary conditions are taken into account, this
can be turned off using the -nopbc option.
With the -tv option the total volume and density of the molecule can
be computed. Please consider whether the normal probe radius is
appropriate 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, in e.g. ice Ih one can easily fit water molecules in the
pores which would yield too low volume, too high surface area and too
-f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt
-s topol.tpr Input
Run input file: tpr tpb tpa
-o area.xvg Output
-or resarea.xvg Output, Opt.
-oa atomarea.xvg Output, Opt.
-tv volume.xvg Output, Opt.
-q connelly.pdb Output, Opt.
Protein data bank file
-n index.ndx Input, Opt.
-i surfat.itp Output, Opt.
Include file for topology
Print help info and quit
-nice int 19
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)
View output xvg, xpm, eps and pdb files
Add specific codes (legends etc.) in the output xvg files for the
-probe real 0.14
Radius of the solvent probe (nm)
-ndots int 24
Number of dots per sphere, more dots means more accuracy
-qmax real 0.2
The maximum charge (e, absolute value) of a hydrophobic atom
Determine from a group in the index file what are the hydrophobic
atoms rather than from the charge
-minarea real 0.5
The minimum area (nm2) to count an atom as a surface atom when writing
a position restraint file (see help)
Take periodicity into account
Output the protein to the connelly pdb file too
-dgs real 0
default value for solvation free energy per area (kJ/mol/nm2)
More information about GROMACS is available at
Thu 16 Oct 2008 g_sas(1)