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x2topMain Table of Contents |
VERSION 3.1
Thu 28 Feb 2002
| VERSION 3.1 |
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 |
| -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 |
| -[no]X | bool | no | Use dialog box GUI to edit command line options |
| -nice | int | 0 | Set the nicelevel |
| -scale | real | 1.1 | Scaling factor for bonds with unknown atom types relative to atom type O |
| -nexcl | int | 3 | Number of exclusions |
| -[no]H14 | bool | no | Use 3rd neighbour interactions for hydrogen atoms |
| -[no]alldih | bool | no | Generate all proper dihedrals |
| -[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. Please set the GMXFULLPBC environment variable as well. |
| -[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) |