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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>pdb2gmx</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 This program reads a <a href="pdb.html">pdb</a> (or <a href="gro.html">gro</a>) file, reads
  18 some database files, adds hydrogens to the molecules and generates
  19 coordinates in Gromacs (Gromos), or optionally <a href="pdb.html">pdb</a>, format
  20 and a topology in Gromacs format.
  21 These files can subsequently be processed to generate a run input file.
  22 <p>
  23 pdb2gmx will search for force fields by looking for
  24 a <tt>forcefield.<a href="itp.html">itp</a></tt> file in subdirectories <tt>&lt;forcefield&gt;.ff</tt>
  25 of the current working directory and of the Gomracs library directory
  26 as inferred from the path of the binary or the <tt>GMXLIB</tt> environment
  27 variable.
  28 By default the forcefield selection is interactive,
  29 but you can use the <tt>-ff</tt> option to specify one of the short names
  30 in the list on the command line instead. In that case pdb2gmx just looks
  31 for the corresponding <tt>&lt;forcefield&gt;.ff</tt> directory.
  32 <p>
  33 After choosing a force field, all files will be read only from
  34 the corresponding force field directory.
  35 If you want to modify or add a residue types, you can copy the force
  36 field directory from the Gromacs library directory to your current
  37 working directory. If you want to add new protein residue types,
  38 you will need to modify residuetypes.<a href="dat.html">dat</a> in the libary directory
  39 or copy the whole library directory to a local directory and set
  40 the environment variable <tt>GMXLIB</tt> to the name of that directory.
  41 Check chapter 5 of the manual for more information about file formats.
  42 <p>
  43 Note that a <a href="pdb.html">pdb</a> file is nothing more than a file format, and it
  44 need not necessarily contain a protein structure. Every kind of
  45 molecule for which there is support in the database can be converted.
  46 If there is no support in the database, you can add it yourself.<p>
  47 The program has limited intelligence, it reads a number of database
  48 files, that allow it to make special bonds (Cys-Cys, Heme-His, etc.),
  49 if necessary this can be done manually. The program can prompt the
  50 user to select which kind of LYS, ASP, GLU, CYS or HIS residue she
  51 wants. For LYS the choice is between neutral (two protons on NZ) or
  52 protonated (three protons, default), for ASP and GLU unprotonated
  53 (default) or protonated, for HIS the proton can be either on ND1,
  54 on NE2 or on both. By default these selections are done automatically.
  55 For His, this is based on an optimal hydrogen bonding
  56 conformation. Hydrogen bonds are defined based on a simple geometric
  57 criterium, specified by the maximum hydrogen-donor-acceptor angle
  58 and donor-acceptor distance, which are set by <tt>-angle</tt> and
  59 <tt>-dist</tt> respectively.<p>
  60 The separation of chains is not entirely trivial since the markup
  61 in user-generated PDB files frequently varies and sometimes it
  62 is desirable to merge entries across a TER record, for instance
  63 if you want a disulfide bridge or distance restraints between
  64 two protein chains or if you have a HEME group bound to a protein.
  65 In such cases multiple chains should be contained in a single
  66 <tt>molecule_type</tt> definition.
  67 To handle this, pdb2gmx has an option <tt>-chainsep</tt> so you can
  68 choose whether a new chain should start when we find a TER record,
  69 when the chain id changes, combinations of either or both of these
  70 or fully interactively.<p>
  71 pdb2gmx will also check the occupancy field of the <a href="pdb.html">pdb</a> file.
  72 If any of the occupancies are not one, indicating that the atom is
  73 not resolved well in the structure, a warning message is issued.
  74 When a <a href="pdb.html">pdb</a> file does not originate from an X-Ray structure determination
  75 all occupancy fields may be zero. Either way, it is up to the user
  76 to verify the correctness of the input data (read the article!).<p>
  77 During processing the atoms will be reordered according to Gromacs
  78 conventions. With <tt>-n</tt> an index file can be generated that
  79 contains one group reordered in the same way. This allows you to
  80 convert a Gromos trajectory and coordinate file to Gromos. There is
  81 one limitation: reordering is done after the hydrogens are stripped
  82 from the input and before new hydrogens are added. This means that
  83 you should not use <tt>-ignh</tt>.<p>
  84 The <tt>.<a href="gro.html">gro</a></tt> and <tt>.<a href="g96.html">g96</a></tt> file formats do not support chain
  85 identifiers. Therefore it is useful to enter a <a href="pdb.html">pdb</a> file name at
  86 the <tt>-o</tt> option when you want to convert a multichain <a href="pdb.html">pdb</a> file.
  87 <p>
  88 The option <tt>-vsite</tt> removes hydrogen and fast improper dihedral
  89 motions. Angular and out-of-plane motions can be removed by changing
  90 hydrogens into virtual sites and fixing angles, which fixes their
  91 position relative to neighboring atoms. Additionally, all atoms in the
  92 aromatic rings of the standard amino acids (i.e. PHE, TRP, TYR and HIS)
  93 can be converted into virtual sites, elminating the fast improper dihedral
  94 fluctuations in these rings. Note that in this case all other hydrogen
  95 atoms are also converted to virtual sites. The mass of all atoms that are
  96 converted into virtual sites, is added to the heavy atoms.<p>
  97 Also slowing down of dihedral motion can be done with <tt>-heavyh</tt>
  98 done by increasing the hydrogen-mass by a factor of 4. This is also
  99 done for water hydrogens to slow down the rotational motion of water.
 100 The increase in mass of the hydrogens is subtracted from the bonded
 101 (heavy) atom so that the total mass of the system remains the same.
 102 <P>
 103 <H3>Files</H3>
 104 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
 105 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
 106 <TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   eiwit.pdb</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>
 107 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">    conf.gro</a></tt> </TD><TD> Output </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> etc. </TD></TR>
 108 <TR><TD ALIGN=RIGHT> <b><tt>-p</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="top.html">   topol.top</a></tt> </TD><TD> Output </TD><TD> Topology file </TD></TR>
 109 <TR><TD ALIGN=RIGHT> <b><tt>-i</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="itp.html">   posre.itp</a></tt> </TD><TD> Output </TD><TD> Include file for topology </TD></TR>
 110 <TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">   clean.ndx</a></tt> </TD><TD> Output, Opt. </TD><TD> Index file </TD></TR>
 111 <TR><TD ALIGN=RIGHT> <b><tt>-q</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   clean.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> etc. </TD></TR>
 112 </TABLE>
 113 <P>
 114 <H3>Other options</H3>
 115 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
 116 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
 117 <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>
 118 <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>
 119 <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>
 120 <TR><TD ALIGN=RIGHT> <b><tt>-chainsep</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>id_or_ter</tt> </TD><TD> Condition in PDB files when a new chain and molecule_type should be started: <tt>id_or_ter</tt>, <tt>id_and_ter</tt>, <tt>ter</tt>, <tt>id</tt> or <tt>interactive</tt> </TD></TD>
 121 <TR><TD ALIGN=RIGHT> <b><tt>-ff</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>select</tt> </TD><TD> Force field, interactive by default. Use -h for information. </TD></TD>
 122 <TR><TD ALIGN=RIGHT> <b><tt>-water</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>select</tt> </TD><TD> Water model to use: <tt>select</tt>, <tt>none</tt>, <tt>spc</tt>, <tt>spce</tt>, <tt>tip3p</tt>, <tt>tip4p</tt> or <tt>tip5p</tt> </TD></TD>
 123 <TR><TD ALIGN=RIGHT> <b><tt>-[no]inter</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Set the next 8 options to interactive </TD></TD>
 124 <TR><TD ALIGN=RIGHT> <b><tt>-[no]ss</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Interactive SS bridge selection </TD></TD>
 125 <TR><TD ALIGN=RIGHT> <b><tt>-[no]ter</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Interactive termini selection, iso charged </TD></TD>
 126 <TR><TD ALIGN=RIGHT> <b><tt>-[no]lys</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Interactive Lysine selection, iso charged </TD></TD>
 127 <TR><TD ALIGN=RIGHT> <b><tt>-[no]arg</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Interactive Arganine selection, iso charged </TD></TD>
 128 <TR><TD ALIGN=RIGHT> <b><tt>-[no]asp</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Interactive Aspartic Acid selection, iso charged </TD></TD>
 129 <TR><TD ALIGN=RIGHT> <b><tt>-[no]glu</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Interactive Glutamic Acid selection, iso charged </TD></TD>
 130 <TR><TD ALIGN=RIGHT> <b><tt>-[no]gln</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Interactive Glutamine selection, iso neutral </TD></TD>
 131 <TR><TD ALIGN=RIGHT> <b><tt>-[no]his</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Interactive Histidine selection, iso checking H-bonds </TD></TD>
 132 <TR><TD ALIGN=RIGHT> <b><tt>-angle</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>135   </tt> </TD><TD> Minimum hydrogen-donor-acceptor angle for a H-bond (degrees) </TD></TD>
 133 <TR><TD ALIGN=RIGHT> <b><tt>-dist</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.3   </tt> </TD><TD> Maximum donor-acceptor distance for a H-bond (nm) </TD></TD>
 134 <TR><TD ALIGN=RIGHT> <b><tt>-[no]una</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Select aromatic rings with united CH atoms on Phenylalanine, Tryptophane and Tyrosine </TD></TD>
 135 <TR><TD ALIGN=RIGHT> <b><tt>-[no]ignh</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Ignore hydrogen atoms that are in the <a href="pdb.html">pdb</a> file </TD></TD>
 136 <TR><TD ALIGN=RIGHT> <b><tt>-[no]missing</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Continue when atoms are missing, dangerous </TD></TD>
 137 <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> Be slightly more verbose in messages </TD></TD>
 138 <TR><TD ALIGN=RIGHT> <b><tt>-posrefc</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1000  </tt> </TD><TD> Force constant for position restraints </TD></TD>
 139 <TR><TD ALIGN=RIGHT> <b><tt>-vsite</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Convert atoms to virtual sites: <tt>none</tt>, <tt>hydrogens</tt> or <tt>aromatics</tt> </TD></TD>
 140 <TR><TD ALIGN=RIGHT> <b><tt>-[no]heavyh</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Make hydrogen atoms heavy </TD></TD>
 141 <TR><TD ALIGN=RIGHT> <b><tt>-[no]deuterate</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Change the mass of hydrogens to 2 amu </TD></TD>
 142 <TR><TD ALIGN=RIGHT> <b><tt>-[no]chargegrp</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Use charge groups in the <a href="rtp.html">rtp</a> file </TD></TD>
 143 <TR><TD ALIGN=RIGHT> <b><tt>-[no]cmap</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Use cmap torsions (if enabled in the <a href="rtp.html">rtp</a> file) </TD></TD>
 144 <TR><TD ALIGN=RIGHT> <b><tt>-[no]renum</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Renumber the residues consecutively in the output </TD></TD>
 145 <TR><TD ALIGN=RIGHT> <b><tt>-[no]rtpres</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Use <a href="rtp.html">rtp</a> entry names as residue names </TD></TD>
 146 </TABLE>
 147 <P>
 148 <hr>
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