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.
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 to specify input files:
Options to specify output files:
Other options: