NAME
x2top - generates a primitive topology from coordinates
VERSION 4.0.1
SYNOPSIS
x2top -f conf.gro -o out.top -r out.rtp -[no]h -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
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
supported currently are:
G43a1 GROMOS96 43a1 Forcefield (official distribution)
oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
G43b1 GROMOS96 43b1 Vacuum Forcefield (official distribution)
gmx Gromacs Forcefield (a modified GROMOS87, see manual)
G43a2 GROMOS96 43a2 Forcefield (development) (improved alkane
dihedrals)
The corresponding data files can be found in the library directory with
names like ffXXXX.YYY. Check chapter 5 of the manual for more
information about file formats. By default the forcefield 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 pdb2gmx
just looks for the corresponding file.
FILES
-f conf.gro Input
Structure file: gro g96 pdb tpr tpb tpa
-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
-nice int 0
Set the nicelevel
-ff string oplsaa
Force field for your simulation. Type "select" for interactive
selcection.
-[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 (ffG43a1.n2t
file in the $GMXLIB 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/>.
Thu 16 Oct 2008 x2top(1)