g_sas(1)
NAME
g_sas - computes solvent accessible surface area
SYNOPSIS
g_sas -f traj.xtc -s topol.tpr -o area.xvg -or resarea.xvg -oa atomarea.xvg -q connelly.pdb -n index.ndx -i surfat.itp -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -solsize 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 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 nonsolvent 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 -pbc option.
FILES
- -f traj.xtc Input
- Generic trajectory: xtc trr trj gro g96 pdb
- -s topol.tpr Input
- Generic run input: tpr tpb tpa xml
- -o area.xvg Output
- xvgr/xmgr file
- -or resarea.xvg Output, Opt.
- xvgr/xmgr file
- -oa atomarea.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]h no
- 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)
- -[no]w no
- View output xvg, xpm, eps and pdb files
- -[no]xvgr yes
- Add specific codes (legends etc.) in the output xvg files for the
- xmgrace program
- -solsize 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_index no
- 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]pbc yes
- Take periodicity into account
- -[no]prot yes
- 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
- More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.