| VERSION 3.2.0 |
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.
option | filename | type | description |
---|---|---|---|
-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 |
option | type | default | description |
---|---|---|---|
-[no]h | bool | 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 | bool | yes | Use 3rd neighbour interactions for hydrogen atoms |
-[no]alldih | bool | no | Generate all proper dihedrals |
-[no]remdih | bool | no | Remove dihedrals on the same bond as an improper |
-[no]pairs | bool | yes | Output 1-4 interactions (pairs) in topology file |
-name | string | ICE | Name of your molecule |
-[no]pbc | bool | yes | Use periodic boundary conditions. |
-[no]param | bool | no | Print parameters in the output |
-[no]round | bool | 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) |