Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages


home | help
GMX-X2TOP(1)			    GROMACS			  GMX-X2TOP(1)

       gmx-x2top - Generate a primitive	topology from coordinates

	  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_]

       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 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>] ( (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

       -[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)

       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.


       More	information    about	GROMACS	   is	 available    at    <->.

       2020, GROMACS development team

2020.3				 Jul 09, 2020			  GMX-X2TOP(1)


Want to link to this manual page? Use this URL:

home | help