NAME

       g_x2top - generates a primitive topology from coordinates VERSION 4.6.5

SYNOPSIS

       g_x2top  -f  conf.gro  -o  out.top  -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

DESCRIPTION

         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 database.

       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.

FILES

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

       -o out.top Output, Opt.
        Topology file

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

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        Print version info and quit

       -nice int 0
        Set the nicelevel

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

       -[no]vno
        Generate verbose output in the top file.

       -nexcl int 3
        Number of exclusions

       -[no]H14yes
        Use 3rd neighbour interactions for hydrogen atoms

       -[no]alldihno
        Generate all proper dihedrals

       -[no]remdihno
        Remove dihedrals on the same bond as an improper

       -[no]pairsyes
        Output 1-4 interactions (pairs) in topology file

       -name string ICE
        Name of your molecule

       -[no]pbcyes
        Use periodic boundary conditions.

       -[no]pdbqno
        Use the B-factor supplied in a  .pdb file for the atomic charges

       -[no]paramyes
        Print parameters in the output

       -[no]roundyes
        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)

KNOWN PROBLEMS

       - 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.

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

                                                 Mon 2 Dec 2013                                       g_x2top(1)