g_sas(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_sas(1)
NAME
g_sas - computes solvent accessible surface area
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
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 -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -probe real -ndots int -qmax real -[no]f_index -minarea real
-[no]pbc -[no]prot -dgs real
DESCRIPTION
g_sas computes hydrophobic, hydrophilic and total solvent accessible surface area. As a side effect, the Connolly surface can be gener-
ated 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 average and standard devia-
tion of the area over the trajectory 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. 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.
FILES
-f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt
-s topol.tpr Input
Structure+mass(db): tpr tpb tpa gro g96 pdb
-o area.xvg Output
xvgr/xmgr file
-or resarea.xvg Output, Opt.
xvgr/xmgr file
-oa atomarea.xvg Output, Opt.
xvgr/xmgr file
-tv volume.xvg Output, Opt.
xvgr/xmgr file
-q connelly.pdb Output, Opt.
Protein data bank file
-n index.ndx Input, Opt.
Index file
-i surfat.itp Output, Opt.
Include file for topology
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version 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)
-[no]wno
View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none
-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
-[no]f_indexno
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)
-[no]pbcyes
Take periodicity into account
-[no]protyes
Output the protein to the Connelly .pdb file too
-dgs real 0
Default value for solvation free energy per area (kJ/mol/nm2)
SEE ALSO
gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_sas(1)