:-)  G  R  O  M  A  C  S  (-:

                   GROningen MAchine for Chemical Simulation

                            :-)  VERSION 4.5.1  (-:

        Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
      Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, 
        Gerrit Groenhof, Peter Kasson, Per Larsson, Peiter Meulenhoff, 
          Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schultz, 
                Michael Shirts, Alfons Sijbers, Peter Tieleman,

               Berk Hess, David van der Spoel, and Erik Lindahl.

       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
            Copyright (c) 2001-2010, The GROMACS development team at
        Uppsala University & The Royal Institute of Technology, Sweden.
            check out http://www.gromacs.org for more information.

         This program is free software; you can redistribute it and/or
          modify it under the terms of the GNU General Public License
         as published by the Free Software Foundation; either version 2
             of the License, or (at your option) any later version.

                               :-)  pdb2gmx  (-:

Option     Filename  Type         Description
------------------------------------------------------------
  -f   cpeptide.pdb  Input        Structure file: gro g96 pdb tpr etc.
  -o   cpeptide.gro  Output       Structure file: gro g96 pdb etc.
  -p   cpeptide.top  Output       Topology file
  -i      posre.itp  Output       Include file for topology
  -n      clean.ndx  Output, Opt. Index file
  -q      clean.pdb  Output, Opt. Structure file: gro g96 pdb etc.

Option       Type   Value   Description
------------------------------------------------------
-[no]h       bool   no      Print help info and quit
-[no]version bool   no      Print version info and quit
-nice        int    0       Set the nicelevel
-chainsep    enum   id_or_ter  Condition in PDB files when a new chain and
                            molecule_type should be started: id_or_ter,
                            id_and_ter, ter, id or interactive
-ff          string select  Force field, interactive by default. Use -h for
                            information.
-water       enum   select  Water model to use: select, none, spc, spce,
                            tip3p, tip4p or tip5p
-[no]inter   bool   no      Set the next 8 options to interactive
-[no]ss      bool   no      Interactive SS bridge selection
-[no]ter     bool   no      Interactive termini selection, iso charged
-[no]lys     bool   no      Interactive Lysine selection, iso charged
-[no]arg     bool   no      Interactive Arganine selection, iso charged
-[no]asp     bool   no      Interactive Aspartic Acid selection, iso charged
-[no]glu     bool   no      Interactive Glutamic Acid selection, iso charged
-[no]gln     bool   no      Interactive Glutamine selection, iso neutral
-[no]his     bool   no      Interactive Histidine selection, iso checking
                            H-bonds
-angle       real   135     Minimum hydrogen-donor-acceptor angle for a
                            H-bond (degrees)
-dist        real   0.3     Maximum donor-acceptor distance for a H-bond (nm)
-[no]una     bool   no      Select aromatic rings with united CH atoms on
                            Phenylalanine, Tryptophane and Tyrosine
-[no]ignh    bool   no      Ignore hydrogen atoms that are in the pdb file
-[no]missing bool   no      Continue when atoms are missing, dangerous
-[no]v       bool   no      Be slightly more verbose in messages
-posrefc     real   1000    Force constant for position restraints
-vsite       enum   none    Convert atoms to virtual sites: none, hydrogens
                            or aromatics
-[no]heavyh  bool   no      Make hydrogen atoms heavy
-[no]deuterate bool no      Change the mass of hydrogens to 2 amu
-[no]chargegrp bool yes     Use charge groups in the rtp file
-[no]cmap    bool   yes     Use cmap torsions (if enabled in the rtp file)
-[no]renum   bool   no      Renumber the residues consecutively in the output
-[no]rtpres  bool   no      Use rtp entry names as residue names