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 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 gmx x2top just looks for the corresponding 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 selection.

       -[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

       2025, GROMACS development team

2025.2                                            May 12, 2025                                      GMX-X2TOP(1)