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GMX-X2TOP(1)			    GROMACS			  GMX-X2TOP(1)

NAME
       gmx-x2top - Generate a primitive	topology from coordinates

SYNOPSIS
	  gmx x2top [-f	[_.gro/.g96/..._]] [-o [_.top_]] [-r [_.rtp_]]
		    [-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	files:

       -f [<.gro/.g96/^a|>] (conf.gro)
	      Structure	file: gro g96 pdb brk ent esp tpr

       Options to specify output files:

       -o [<.top>] (out.top) (Optional)
	      Topology file

       -r [<.rtp>] (out.rtp) (Optional)
	      Residue Type file	used by	pdb2gmx

       Other options:

       -ff <string> (oplsaa)
	      Force  field  for	your simulation. Type aselecta for interactive
	      selection.

       -[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/nm^2)

       -kt <real> (400)
	      Angle force constant (kJ/mol/rad^2)

       -kp <real> (5)
	      Dihedral angle force constant (kJ/mol/rad^2)

KNOWN ISSUES
       o The atom type selection is primitive. Virtually no chemical knowledge
	 is used

       o Periodic boundary conditions screw up the bonding

       o No improper dihedrals are generated

       o 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
       gmx(1)

       More	information    about	GROMACS	   is	 available    at    <-
       http://www.gromacs.org/>.

COPYRIGHT
       2020, GROMACS development team

2020.3				 Jul 09, 2020			  GMX-X2TOP(1)

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

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