man x2top (Commandes) - x2top VERSION 3.3_beta_20050823
NAME
x2top VERSION 3.3_beta_20050823
SYNOPSIS
x2top -f conf.gro -o out.top -r out.rtp -[no]h -nice int -scale real -ff string -nexcl int -[no]H14 -[no]alldih -[no]remdih -[no]pairs -name string -[no]pbc -[no]param -[no]round -kb real -kt real -kp real
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.The force fields supported currently are:
G43a1 GROMOS96 43a1 Forcefield (official distribution)
oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
G43b1 GROMOS96 43b1 Vacuum Forcefield (official distribution)
gmx Gromacs Forcefield (a modified GROMOS87, see manual)
G43a2 GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
The corresponding data files can be found in the library directory with names like ffXXXX.YYY. Check chapter 5 of the manual for more information about file formats. By default the forcefield selection is interactive, but you can use the -ff option to specify one of the short names above on the command line instead. In that case pdb2gmx just looks for the corresponding file.
FILES
-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
-[no]h 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 string select Select the force field for your simulation.
-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]param no 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)
- 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 (ffG43a1.n2t file in the $GMXLIB directory). Please extend it and send the results back to the GROMACS crew.