g_sas(1)

NAME
g_sas VERSION 3.2.0

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 -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 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 -1
 First frame (ps) to read from trajectory -e time -1
 Last frame (ps) to read from trajectory -dt time -1
 Only use frame when t MOD dt = first time (ps) -[no]w no
 View output xvg, xpm, eps and pdb files -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)