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>]
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.
-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
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
gmx x2top just looks for the corresponding file.
Options to specify input files:
Options to specify output files:
-o[<.top>] (out.top) (Optional)
-r[<.rtp>] (out.rtp) (Optional)
Residue Type file used by pdb2gmx
Force field for your simulation. Type “select” for interactive selection.
Generate verbose output in the top file.
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 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
Bonded force constant (kJ/mol/nm^2)
Angle force constant (kJ/mol/rad^2)
Dihedral angle force constant (kJ/mol/rad^2)
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.n2tfile in the data directory). Please extend it and send the results back to the GROMACS crew.