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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_sas</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
  12 </TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
  13 Thu 26 Aug 2010</B></td></tr></TABLE>
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  15 <H3>Description</H3>
  16 <p>
  17 g_sas computes hydrophobic, hydrophilic and total solvent accessible surface area.
  18 As a side effect the Connolly surface can be generated as well in
  19 a <a href="pdb.html">pdb</a> file where the nodes are represented as atoms and the vertices
  20 connecting the nearest nodes as CONECT records.
  21 The program will ask for a group for the surface calculation
  22 and a group for the output. The calculation group should always
  23 consists of all the non-solvent atoms in the system.
  24 The output group can be the whole or part of the calculation group.
  25 The area can be plotted
  26 per residue and atom as well (options <tt>-or</tt> and <tt>-oa</tt>).
  27 In combination with the latter option an <tt><a href="itp.html">itp</a></tt> file can be
  28 generated (option <tt>-i</tt>)
  29 which can be used to restrain surface atoms.<p>
  30 By default, periodic boundary conditions are taken into account,
  31 this can be turned off using the <tt>-nopbc</tt> option.<p>
  32 With the <tt>-tv</tt> option the total volume and density of the molecule can be
  33 computed.
  34 Please consider whether the normal probe radius is appropriate
  35 in this case or whether you would rather use e.g. 0. It is good
  36 to keep in mind that the results for volume and density are very
  37 approximate, in e.g. ice Ih one can easily fit water molecules in the
  38 pores which would yield too low volume, too high surface area and too
  39 high density.
  40 <P>
  41 <H3>Files</H3>
  42 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  43 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  44 <TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">    traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
  45 <TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
  46 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">    area.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  47 <TR><TD ALIGN=RIGHT> <b><tt>-or</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> resarea.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  48 <TR><TD ALIGN=RIGHT> <b><tt>-oa</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">atomarea.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  49 <TR><TD ALIGN=RIGHT> <b><tt>-tv</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">  volume.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  50 <TR><TD ALIGN=RIGHT> <b><tt>-q</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html">connelly.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Protein data bank file </TD></TR>
  51 <TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">   index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
  52 <TR><TD ALIGN=RIGHT> <b><tt>-i</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="itp.html">  surfat.itp</a></tt> </TD><TD> Output, Opt. </TD><TD> Include file for topology </TD></TR>
  53 </TABLE>
  54 <P>
  55 <H3>Other options</H3>
  56 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  57 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  58 <TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print help info and quit </TD></TD>
  59 <TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print version info and quit </TD></TD>
  60 <TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
  61 <TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
  62 <TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
  63 <TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
  64 <TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
  65 <TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
  66 <TR><TD ALIGN=RIGHT> <b><tt>-probe</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.14  </tt> </TD><TD> Radius of the solvent probe (nm) </TD></TD>
  67 <TR><TD ALIGN=RIGHT> <b><tt>-ndots</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>24</tt> </TD><TD> Number of dots per sphere, more dots means more accuracy </TD></TD>
  68 <TR><TD ALIGN=RIGHT> <b><tt>-qmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.2   </tt> </TD><TD> The maximum charge (e, absolute value) of a hydrophobic atom </TD></TD>
  69 <TR><TD ALIGN=RIGHT> <b><tt>-[no]f_index</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Determine from a group in the index file what are the hydrophobic atoms rather than from the charge </TD></TD>
  70 <TR><TD ALIGN=RIGHT> <b><tt>-minarea</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.5   </tt> </TD><TD> The minimum area (nm^2) to count an atom as a surface atom when writing a position restraint file  (see help) </TD></TD>
  71 <TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Take periodicity into account </TD></TD>
  72 <TR><TD ALIGN=RIGHT> <b><tt>-[no]prot</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Output the protein to the connelly <a href="pdb.html">pdb</a> file too </TD></TD>
  73 <TR><TD ALIGN=RIGHT> <b><tt>-dgs</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> default value for solvation free energy per area (kJ/mol/nm^2) </TD></TD>
  74 </TABLE>
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