x2top

Main Table of Contents

VERSION 3.2.0
Sun 25 Jan 2004


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.

Files

optionfilenametypedescription
-f conf.gro Input Generic structure: gro g96 pdb tpr tpb tpa xml
-o out.top Output, Opt. Topology file
-r out.rtp Output, Opt. Residue Type file used by pdb2gmx

Other options

optiontypedefaultdescription
-[no]h bool no Print help info and quit
-nice int 0 Set the nicelevel
-scale real 1.1 Scaling factor for bonds with unknown atom types relative to atom type O
-ff enum G43a1 Select the force field for your simulation: G43a1, oplsaa, gmx, G43a2 or G43b1
-nexcl int 3 Number of exclusions
-[no]H14 bool yes Use 3rd neighbour interactions for hydrogen atoms
-[no]alldih bool no Generate all proper dihedrals
-[no]remdih bool no Remove dihedrals on the same bond as an improper
-[no]pairs bool yes Output 1-4 interactions (pairs) in topology file
-name string ICE Name of your molecule
-[no]pbc bool yes Use periodic boundary conditions.
-[no]param bool no Print parameters in the output
-[no]round bool 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)


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