1g_x2top(1)                GROMACS suite, VERSION 4.5                g_x2top(1)
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NAME

6       g_x2top - generates a primitive topology from coordinates
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8       VERSION 4.5
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SYNOPSIS

11       g_x2top -f conf.gro -o out.top -r out.rtp -[no]h -[no]version -nice int
12       -ff  string  -[no]v  -nexcl  int   -[no]H14   -[no]alldih   -[no]remdih
13       -[no]pairs  -name  string  -[no]pbc -[no]pdbq -[no]param -[no]round -kb
14       real -kt real -kp real
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DESCRIPTION

17       x2top generates a primitive topology from a coordinate file.  The  pro‐
18       gram  assumes all hydrogens are present when defining the hybridization
19       from the atom name and the number of bonds.  The program can also  make
20       an rtp entry, which you can then add to the rtp database.
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23       When   -param  is  set, equilibrium distances and angles and force con‐
24       stants will be printed in the topology for all interactions. The  equi‐
25       librium  distances and angles are taken from the input coordinates, the
26       force constant are set with command line  options.   The  force  fields
27       somewhat supported currently are:
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30       G53a5  GROMOS96 53a5 Forcefield (official distribution)
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33       oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
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36       The corresponding data files can be found in the library directory with
37       name atomname2type.n2t. Check chapter 5 of the manual for more informa‐
38       tion  about file formats. By default the forcefield selection is inter‐
39       active, but you can use the  -ff option to specify  one  of  the  short
40       names  above  on  the  command  line instead. In that case pdb2gmx just
41       looks for the corresponding file.
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FILES

46       -f conf.gro Input
47        Structure file: gro g96 pdb tpr etc.
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49       -o out.top Output, Opt.
50        Topology file
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52       -r out.rtp Output, Opt.
53        Residue Type file used by pdb2gmx
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OTHER OPTIONS

57       -[no]hno
58        Print help info and quit
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60       -[no]versionno
61        Print version info and quit
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63       -nice int 0
64        Set the nicelevel
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66       -ff string oplsaa
67        Force field for your simulation. Type "select" for interactive  selec‐
68       tion.
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70       -[no]vno
71        Generate verbose output in the top file.
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73       -nexcl int 3
74        Number of exclusions
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76       -[no]H14yes
77        Use 3rd neighbour interactions for hydrogen atoms
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79       -[no]alldihno
80        Generate all proper dihedrals
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82       -[no]remdihno
83        Remove dihedrals on the same bond as an improper
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85       -[no]pairsyes
86        Output 1-4 interactions (pairs) in topology file
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88       -name string ICE
89        Name of your molecule
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91       -[no]pbcyes
92        Use periodic boundary conditions.
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94       -[no]pdbqno
95        Use the B-factor supplied in a pdb file for the atomic charges
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97       -[no]paramyes
98        Print parameters in the output
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100       -[no]roundyes
101        Round off measured values
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103       -kb real 400000
104        Bonded force constant (kJ/mol/nm2)
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106       -kt real 400
107        Angle force constant (kJ/mol/rad2)
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109       -kp real 5
110        Dihedral angle force constant (kJ/mol/rad2)
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KNOWN PROBLEMS

114       - The atom type selection is primitive. Virtually no chemical knowledge
115       is used
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117       - Periodic boundary conditions screw up the bonding
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119       - No improper dihedrals are generated
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121       -  The  atoms  to  atomtype  translation  table  is  incomplete  (atom‐
122       name2type.n2t  files  in the data directory). Please extend it and send
123       the results back to the GROMACS crew.
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SEE ALSO

127       gromacs(7)
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129       More  information  about  GROMACS  is  available  at   <http://www.gro‐
130       macs.org/>.
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134                                Thu 26 Aug 2010                     g_x2top(1)
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