1 .TH x2top 1 "Thu 16 Oct 2008"
3 x2top - generates a primitive topology from coordinates
20 .BI "-name" " string "
29 x2top generates a primitive topology from a coordinate file.
30 The program assumes all hydrogens are present when defining
31 the hybridization from the atom name and the number of bonds.
32 The program can also make an rtp entry, which you can then add
38 is set, equilibrium distances and angles
39 and force constants will be printed in the topology for all
40 interactions. The equilibrium distances and angles are taken
41 from the input coordinates, the force constant are set with
42 command line options.The force fields supported currently are:
45 G43a1 GROMOS96 43a1 Forcefield (official distribution)
48 oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
51 G43b1 GROMOS96 43b1 Vacuum Forcefield (official distribution)
54 gmx Gromacs Forcefield (a modified GROMOS87, see manual)
57 G43a2 GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
60 The corresponding data files can be found in the library directory
61 with names like ffXXXX.YYY. Check chapter 5 of the manual for more
62 information about file formats. By default the forcefield selection
63 is interactive, but you can use the
66 one of the short names above on the command line instead. In that
67 case pdb2gmx just looks for the corresponding file.
73 Structure file: gro g96 pdb tpr tpb tpa
81 Residue Type file used by pdb2gmx
85 Print help info and quit
87 .BI "-nice" " int" " 0"
90 .BI "-ff" " string" " oplsaa"
91 Force field for your simulation. Type "select" for interactive selcection.
94 Generate verbose output in the top file.
96 .BI "-nexcl" " int" " 3"
100 Use 3rd neighbour interactions for hydrogen atoms
102 .BI "-[no]alldih" "no "
103 Generate all proper dihedrals
105 .BI "-[no]remdih" "no "
106 Remove dihedrals on the same bond as an improper
108 .BI "-[no]pairs" "yes "
109 Output 1-4 interactions (pairs) in topology file
111 .BI "-name" " string" " ICE"
112 Name of your molecule
114 .BI "-[no]pbc" "yes "
115 Use periodic boundary conditions.
117 .BI "-[no]pdbq" "no "
118 Use the B-factor supplied in a pdb file for the atomic charges
120 .BI "-[no]param" "yes "
121 Print parameters in the output
123 .BI "-[no]round" "yes "
124 Round off measured values
126 .BI "-kb" " real" " 400000"
127 Bonded force constant (kJ/mol/nm2)
129 .BI "-kt" " real" " 400 "
130 Angle force constant (kJ/mol/rad2)
132 .BI "-kp" " real" " 5 "
133 Dihedral angle force constant (kJ/mol/rad2)
136 \- The atom type selection is primitive. Virtually no chemical knowledge is used
138 \- Periodic boundary conditions screw up the bonding
140 \- No improper dihedrals are generated
142 \- 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.