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Bash Scripting program

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g_x2top

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)