g_x2top(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_x2top(1)
NAME
g_x2top - generates a primitive topology from coordinates
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
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
DESCRIPTION
g_x2top generates a primitive topology from a coordinate file. The program assumes all hydrogens are present when defining the hybridiza-
tion 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 equi-
librium 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.
FILES
-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
OTHER OPTIONS
-[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)
KNOWN PROBLEMS
- 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.
SEE ALSO
gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_x2top(1)
