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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_x2top</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>
  14 <HR>
  15 <H3>Description</H3>
  16 <p>
  17 <a href="x2top.html">x2top</a> generates a primitive topology from a coordinate file.
  18 The program assumes all hydrogens are present when defining
  19 the hybridization from the atom name and the number of bonds.
  20 The program can also make an <a href="rtp.html">rtp</a> entry, which you can then add
  21 to the <a href="rtp.html">rtp</a> database.<p>
  22 When <tt>-param</tt> is set, equilibrium distances and angles
  23 and force constants will be printed in the topology for all
  24 interactions. The equilibrium distances and angles are taken
  25 from the input coordinates, the force constant are set with
  26 command line options.
  27 The force fields somewhat supported currently are:<p>
  28 G53a5  GROMOS96 53a5 Forcefield (official distribution)<p>
  29 oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)<p>
  30 The corresponding data files can be found in the library directory
  31 with name atomname2type.n2t. Check chapter 5 of the manual for more
  32 information about file formats. By default the forcefield selection
  33 is interactive, but you can use the <tt>-ff</tt> option to specify
  34 one of the short names above on the command line instead. In that
  35 case <a href="pdb2gmx.html">pdb2gmx</a> just looks for the corresponding file.<p>
  36 <P>
  37 <H3>Files</H3>
  38 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  39 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  40 <TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">    conf.gro</a></tt> </TD><TD> Input </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> etc. </TD></TR>
  41 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="top.html">     out.top</a></tt> </TD><TD> Output, Opt. </TD><TD> Topology file </TD></TR>
  42 <TR><TD ALIGN=RIGHT> <b><tt>-r</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="rtp.html">     out.rtp</a></tt> </TD><TD> Output, Opt. </TD><TD> Residue Type file used by <a href="pdb2gmx.html">pdb2gmx</a> </TD></TR>
  43 </TABLE>
  44 <P>
  45 <H3>Other options</H3>
  46 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  47 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  48 <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>
  49 <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>
  50 <TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
  51 <TR><TD ALIGN=RIGHT> <b><tt>-ff</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>oplsaa</tt> </TD><TD> Force field for your simulation. Type "select" for interactive selection. </TD></TD>
  52 <TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Generate verbose output in the <a href="top.html">top</a> file. </TD></TD>
  53 <TR><TD ALIGN=RIGHT> <b><tt>-nexcl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Number of exclusions </TD></TD>
  54 <TR><TD ALIGN=RIGHT> <b><tt>-[no]H14</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Use 3rd neighbour interactions for hydrogen atoms </TD></TD>
  55 <TR><TD ALIGN=RIGHT> <b><tt>-[no]alldih</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Generate all proper dihedrals </TD></TD>
  56 <TR><TD ALIGN=RIGHT> <b><tt>-[no]remdih</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Remove dihedrals on the same bond as an improper </TD></TD>
  57 <TR><TD ALIGN=RIGHT> <b><tt>-[no]pairs</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Output 1-4 interactions (pairs) in topology file </TD></TD>
  58 <TR><TD ALIGN=RIGHT> <b><tt>-name</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>ICE</tt> </TD><TD> Name of your molecule </TD></TD>
  59 <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> Use periodic boundary conditions. </TD></TD>
  60 <TR><TD ALIGN=RIGHT> <b><tt>-[no]pdbq</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Use the B-factor supplied in a <a href="pdb.html">pdb</a> file for the atomic charges </TD></TD>
  61 <TR><TD ALIGN=RIGHT> <b><tt>-[no]param</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Print parameters in the output </TD></TD>
  62 <TR><TD ALIGN=RIGHT> <b><tt>-[no]round</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Round off measured values </TD></TD>
  63 <TR><TD ALIGN=RIGHT> <b><tt>-kb</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>400000</tt> </TD><TD> Bonded force constant (kJ/mol/nm^2) </TD></TD>
  64 <TR><TD ALIGN=RIGHT> <b><tt>-kt</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>400   </tt> </TD><TD> Angle force constant (kJ/mol/rad^2) </TD></TD>
  65 <TR><TD ALIGN=RIGHT> <b><tt>-kp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>5     </tt> </TD><TD> Dihedral angle force constant (kJ/mol/rad^2) </TD></TD>
  66 </TABLE>
  67 <P>
  68 <H3>Known problems</H3>
  69 <UL>
  70 <LI>The atom type selection is primitive. Virtually no chemical knowledge is used
  71 <LI>Periodic boundary conditions screw up the bonding
  72 <LI>No improper dihedrals are generated
  73 <LI>The atoms to atomtype translation table is incomplete (atomname2type.n2t files in the data directory). Please extend it and send the results back to the GROMACS crew.
  74 </UL>
  75 <P>
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