share/html/online/pdb.html

   1 <title>pdb file format</title>
   2 <LINK rel=stylesheet href="style.css" type="text/css">
   3 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
   4 <h2>pdb file format</h2>
   5 <CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
   6 <TR>
   7 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
   8 <TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
   9 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
  10 <TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
  11 <H3>Description</H3>
  12
  13 Files with the <a href="pdb.html">.pdb</a> extension are molecular
  14 structure files in the protein databank file format.  The protein
  15 databank file format describes the positions of atoms in a molecular
  16 structure. Coordinates are read from the ATOM and HETATM records,
  17 until the file ends or an ENDMDL record is encountered.
  18 GROMACS programs can read and write a simlation box in the
  19 CRYST1 entry.
  20 The pdb format can also be used as a trajectory format:
  21 several structures, seperated by ENDMDL, can be read from
  22 or written to one file.
  23
  24 <p>
  25 <h2>Example</h2>
  26 An pdb file should look like this
  27 <PRE>
  28 ATOM      1  H1  LYS     1      14.260   6.590  34.480  1.00  0.00
  29 ATOM      2  H2  LYS     1      13.760   5.000  34.340  1.00  0.00
  30 ATOM      3  N   LYS     1      14.090   5.850  33.800  1.00  0.00
  31 ATOM      4  H3  LYS     1      14.920   5.560  33.270  1.00  0.00
  32 ...
  33 ...
  34 </PRE>
  35
  36 <p>
  37 <a href="../tutor/speptide/speptide.pdb.txt">speptide.pdb</a>:
  38 Protein structure file of Ribonuclease A speptide in protein data
  39 bank file format.
  40
  41 <p>
  42 Links to descriptions of the pdb format
  43 can be found on the <A HREF="../links.html">Links page</A>.
  44
  45 <p>
  46 <hr>
  47 <div ALIGN=RIGHT>
  48 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
  49
  50 </div>
  51
  52 </body>