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GMX-X2TOP(1)			     GROMACS			    GMX-X2TOP(1)

NAME
     gmx-x2top - Generate a primitive topology from coordinates

SYNOPSIS
	gmx x2top [-f [<.gro/.g96/...>]] [-o [<.top>]] [-r [<.rtp>]]
		  [-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
     gmx  x2top generates a primitive topology from a coordinate file.	The pro-
     gram 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  dis-
     tances  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 gmx x2top just looks for the corre-
     sponding file.

OPTIONS
     Options to specify input files:

     -f [<.gro/.g96/...>] (conf.gro)
	    Structure file: gro g96 pdb brk ent esp tpr

     Options to specify output files:

     -o [<.top>] (out.top) (Optional)
	    Topology file

     -r [<.rtp>] (out.rtp) (Optional)
	    Residue Type file used by pdb2gmx

     Other options:

     -ff <string> (oplsaa)
	    Force field for your simulation. Type "select" for	interactive  se-
	    lection.

     -[no]v (no)
	    Generate verbose output in the top file.

     -nexcl <int> (3)
	    Number of exclusions

     -[no]H14 (yes)
	    Use 3rd neighbour interactions for hydrogen atoms

     -[no]alldih (no)
	    Generate all proper dihedrals

     -[no]remdih (no)
	    Remove dihedrals on the same bond as an improper

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

     -name <string> (ICE)
	    Name of your molecule

     -[no]pbc (yes)
	    Use periodic boundary conditions.

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

     -[no]param (yes)
	    Print parameters in the output

     -[no]round (yes)
	    Round off measured values

     -kb <real> (400000)
	    Bonded force constant (kJ/mol/nm^2)

     -kt <real> (400)
	    Angle force constant (kJ/mol/rad^2)

     -kp <real> (5)
	    Dihedral angle force constant (kJ/mol/rad^2)

KNOWN ISSUES
     * 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
     gmx(1)

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

COPYRIGHT
     2026, GROMACS development team

2026.3				  Jun 25, 2026			    GMX-X2TOP(1)
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