Provided by: gromacs-data_4.6.5-1build1_all bug


       g_sas - computes solvent accessible surface area

       VERSION 4.6.5


       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


        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


       -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


        Print help info and quit

        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)

        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

        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 <>.

                                          Mon 2 Dec 2013                                 g_sas(1)