Provided by: gromacs-data_4.6.5-1build1_all bug


       g_x2top - generates a primitive topology from coordinates VERSION 4.6.5


       g_x2top  -f conf.gro -o -r out.rtp -[no]h -[no]version -nice int -ff string -[no]v
       -nexcl int -[no]H14 -[no]alldih -[no]remdih -[no]pairs  -name  string  -[no]pbc  -[no]pdbq
       -[no]param -[no]round -kb real -kt real -kp real


         g_x2top  generates a primitive topology from a coordinate file.  The program assumes all
       hydrogens are present when defining the hybridization from the atom name and the number of
       bonds.   The  program  can  also  make an  .rtp entry, which you can then add to the  .rtp

       When  -param is set, equilibrium distances and angles and force constants will be  printed
       in  the topology for all interactions. The equilibrium distances and angles are taken from
       the input coordinates, the force constant are set with command line  options.   The  force
       fields somewhat supported currently are:

       G53a5  GROMOS96 53a5 Forcefield (official distribution)

       oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)

       The   corresponding   data  files  can  be  found  in  the  library  directory  with  name
       atomname2type.n2t. Check Chapter 5 of the manual for more information about file  formats.
       By  default,  the force field selection is interactive, but you can use the  -ff option to
       specify one of the short names above on the command line instead. In  that  case   g_x2top
       just looks for the corresponding file.


       -f conf.gro Input
        Structure file: gro g96 pdb tpr etc.

       -o Output, Opt.
        Topology file

       -r out.rtp Output, Opt.
        Residue Type file used by pdb2gmx


        Print help info and quit

        Print version info and quit

       -nice int 0
        Set the nicelevel

       -ff string oplsaa
        Force field for your simulation. Type "select" for interactive selection.

        Generate verbose output in the top file.

       -nexcl int 3
        Number of exclusions

        Use 3rd neighbour interactions for hydrogen atoms

        Generate all proper dihedrals

        Remove dihedrals on the same bond as an improper

        Output 1-4 interactions (pairs) in topology file

       -name string ICE
        Name of your molecule

        Use periodic boundary conditions.

        Use the B-factor supplied in a  .pdb file for the atomic charges

        Print parameters in the output

        Round off measured values

       -kb real 400000
        Bonded force constant (kJ/mol/nm2)

       -kt real 400
        Angle force constant (kJ/mol/rad2)

       -kp real 5
        Dihedral angle force constant (kJ/mol/rad2)


       - The atom type selection is primitive. Virtually no chemical knowledge is used

       - Periodic boundary conditions screw up the bonding

       - No improper dihedrals are generated

       -  The  atoms  to atomtype translation table is incomplete ( atomname2type.n2t file in the
       data directory). Please extend it and send the results back to the GROMACS crew.



       More information about GROMACS is available at <>.

                                          Mon 2 Dec 2013                               g_x2top(1)