NAME

       g_sas - computes solvent accessible surface area

       VERSION 4.6.5

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. See Eisenhaber F,
       Lijnzaad P, Argos P, Sander C, & Scharf M (1995) J. Comput. Chem. 16, 273-284.  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 vertice 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 deviation 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 2 Dec 2013                                         g_sas(1)