x2top

Main Table of Contents

VERSION 3.1
Thu 28 Feb 2002


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
-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
-[no]X bool no Use dialog box GUI to edit command line options
-nice int 0 Set the nicelevel
-scale real 1.1 Scaling factor for bonds with unknown atom types relative to atom type O
-nexcl int 3 Number of exclusions
-[no]H14 bool no Use 3rd neighbour interactions for hydrogen atoms
-[no]alldih bool no Generate all proper dihedrals
-[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. Please set the GMXFULLPBC environment variable as well.
-[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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