Provided by: gromacs-data_4.6.5-1build1_all
g_x2top - generates a primitive topology from coordinates VERSION 4.6.5
g_x2top -f conf.gro -o out.top -r out.rtp -[no]h -[no]version -nice int -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
g_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 g_x2top just looks for the corresponding file.
-f conf.gro Input Structure file: gro g96 pdb tpr etc. -o out.top Output, Opt. Topology file -r out.rtp Output, Opt. Residue Type file used by pdb2gmx
-[no]hno Print help info and quit -[no]versionno Print version info and quit -nice int 0 Set the nicelevel -ff string oplsaa Force field for your simulation. Type "select" for interactive selection. -[no]vno Generate verbose output in the top file. -nexcl int 3 Number of exclusions -[no]H14yes Use 3rd neighbour interactions for hydrogen atoms -[no]alldihno Generate all proper dihedrals -[no]remdihno Remove dihedrals on the same bond as an improper -[no]pairsyes Output 1-4 interactions (pairs) in topology file -name string ICE Name of your molecule -[no]pbcyes Use periodic boundary conditions. -[no]pdbqno Use the B-factor supplied in a .pdb file for the atomic charges -[no]paramyes Print parameters in the output -[no]roundyes 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 ( atomname2type.n2t file in the data directory). Please extend it and send the results back to the GROMACS crew.
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 2 Dec 2013 g_x2top(1)