x2top(1)

NAME
x2top VERSION 3.2.0

SYNOPSIS
x2top -f conf.gro -o out.top -r out.rtp -[no]h -nice int -scale real -ff enum -nexcl int -[no]H14 -[no]alldih -[no]remdih -[no]pairs -name string -[no]pbc -[no]param -[no]round -kb real -kt real -kp real

DESCRIPTION
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.

FILES
-f conf.gro Input
 Generic structure: gro g96 pdb tpr tpb tpa xml -o out.top Output, Opt.
 Topology file -r out.rtp Output, Opt.
 Residue Type file used by pdb2gmx

OTHER OPTIONS
-[no]h no
 Print help info and quit -nice int 0
 Set the nicelevel -scale real 1.1
 Scaling factor for bonds with unknown atom types relative to atom type O -ff enum G43a1
 Select the force field for your simulation: G43a1 , oplsaa , gmx , G43a2 or G43b1 -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]param no
 Print parameters in the output -[no]round yes
 Round off measured values -kb real 400000
 Bonded force constant (kJ/mol/nm2) -kt real 400
 Angle force constant (kJ/mol/rad2) -kp real 5
 Dihedral angle force constant (kJ/mol/rad2) - 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 (ffG43a1.n2t file in the $GMXLIB directory). Please extend it and send the results back to the GROMACS crew.