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

       2023, GROMACS development team