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       g_sas - computes solvent accessible surface area

       VERSION 4.0.1


       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  -nice int -b time -e time -dt time -[no]w -[no]xvgr -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.  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
       non-solvent  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  -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, in e.g. ice Ih one can easily fit water molecules  in  the
       pores  which  would yield too low volume, too high surface area and too
       high density.


       -f traj.xtc Input
        Trajectory: xtc trr trj gro g96 pdb cpt

       -s topol.tpr Input
        Run input file: tpr tpb tpa

       -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

       -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

        Add specific codes (legends etc.) in the  output  xvg  files  for  the
       xmgrace program

       -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)



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                                Thu 16 Oct 2008                       g_sas(1)