3 <TITLE>Getting started - Your Own
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11 <td ALIGN=LEFT VALIGN=TOP WIDTH=
280><br><h2>Getting started - Your Own
</h2>
12 <font size=-
1><A HREF=
"../online.html">Main Table of Contents
</A></font><br><br></td>
13 </TABLE></TD><TD WIDTH=
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><p><B>VERSION
4.0<br>
14 Sun
18 Jan
2009</B></td></tr></TABLE>
17 <P><H2><A NAME=
"you">Your own System
</A></H2>
19 For proteins in water (or other solvent) the route is described above.
20 For other systemd (eg. pure liquids or mixtures) one needs:
22 <li> The atomic coordinates, which can be generated by a variety of
23 interactive programs (eg. Quanta, Cerius, HyperChem).
24 Coordinate files can be exported in pdb-format and
25 converted to
<TT><a href=
"gro.html">.gro
</a></TT> format by
26 the
<a href=
"editconf.html">editconf
</a> program:
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33 <tt> editconf -f conf.pdb -o conf.gro
39 where
<TT><a href=
"gro.html">conf.gro
</a></TT> is the coordinatefile,
40 or converted back to pdb-format by
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47 <tt> editconf -f conf.gro -o conf.pdb
53 where
<TT>conf
</TT> is a file with coordinates, and
<TT>
54 <a href=
"pdb.html">conf.pdb
</a></TT> is the target file in
<tt><a href=
"pdb.html">.pdb
</a></tt> format.
55 <b>NOTE:
</b> Make sure that the graphics programs export
56 <b>whole
</b> molecules instead of molecules that are cut in pieces
57 (due to the periodic boundary conditions)
58 If you have the coordinates of single molecules, you can also
59 build systems (pure liquids or mixtures) with
60 <a href=
"genbox.html">genbox
</a>.
61 In contrast, the program
62 <a href=
"genconf.html">genconf
</a>
63 produces the lattice of molecules with random displacements.
64 <li> The topology you have to build yourself. Of course you can
65 include topologies of part of your system (eg.
<TT><a href=
"itp.html">spc.itp
</a></TT>,
66 <TT><a href=
"itp.html">decane.itp
</a></TT> etc.)
70 <a href=
"getting_started.html"><h3>Back to start
</h3></a>