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gmx-x2top(1)			GROMACS	Manual			  gmx-x2top(1)

NAME
       gmx-x2top - Generate a primitive	topology from coordinates

SYNOPSIS
       gmx x2top [-f [<.gro/.g96/...>]]	[-o [<.top>]] [-r [<.rtp>]]
		 [-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
       gmx  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  con-
       stants  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 informa-
       tion about file formats.	By default, the	force field selection  is  in-
       teractive,  but	you can	use the	-ff option to specify one of the short
       names above on the command line instead.	In that	case  gmx  x2top  just
       looks for the corresponding file.

OPTIONS
       Options to specify input	and output files:

       -f [_.gro/.g96/..._] (conf.gro) (Input)
	   Structure file: gro g96 pdb brk ent esp tpr tpb tpa

       -o [_.top_] (out.top) (Output, Optional)
	   Topology file

       -r [_.rtp_] (out.rtp) (Output, Optional)
	   Residue Type	file used by pdb2gmx

       Other options:

       -nice _int_ (0)
	   Set the nicelevel

       -ff _string_ (oplsaa)
	   Force  field	for your simulation. Type "select" for interactive se-
       lection.

       -[no]v  (no)
	   Generate verbose output in the top file.

       -nexcl _int_ (3)
	   Number of exclusions

       -[no]H14	 (yes)
	   Use 3rd neighbour interactions for hydrogen atoms

       -[no]alldih  (no)
	   Generate all	proper dihedrals

       -[no]remdih  (no)
	   Remove dihedrals on the same	bond as	an improper

       -[no]pairs  (yes)
	   Output 1-4 interactions (pairs) in topology file

       -name _string_ (ICE)
	   Name	of your	molecule

       -[no]pbc	 (yes)
	   Use periodic	boundary conditions.

       -[no]pdbq  (no)
	   Use the B-factor supplied in	a .pdb file for	the atomic charges

       -[no]param  (yes)
	   Print parameters in the output

       -[no]round  (yes)
	   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 ISSUES
       - 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	(atom-
       name2type.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.gro-
       macs.org/>.

VERSION	5.0.6							  gmx-x2top(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | KNOWN ISSUES | SEE ALSO

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