1GMX-X2TOP(1)                        GROMACS                       GMX-X2TOP(1)
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NAME

6       gmx-x2top - Generate a primitive topology from coordinates
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SYNOPSIS

9          gmx x2top [-f [<.gro/.g96/...>]] [-o [<.top>]] [-r [<.rtp>]]
10                    [-ff <string>] [-[no]v] [-nexcl <int>] [-[no]H14]
11                    [-[no]alldih] [-[no]remdih] [-[no]pairs] [-name <string>]
12                    [-[no]pbc] [-[no]pdbq] [-[no]param] [-[no]round]
13                    [-kb <real>] [-kt <real>] [-kp <real>]
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DESCRIPTION

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

39       Options to specify input files:
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41       -f [<.gro/.g96/...>] (conf.gro)
42              Structure file: gro g96 pdb brk ent esp tpr
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44       Options to specify output files:
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46       -o [<.top>] (out.top) (Optional)
47              Topology file
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49       -r [<.rtp>] (out.rtp) (Optional)
50              Residue Type file used by pdb2gmx
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52       Other options:
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54       -ff <string> (oplsaa)
55              Force  field  for your simulation. Type "select" for interactive
56              selection.
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58       -[no]v (no)
59              Generate verbose output in the top file.
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61       -nexcl <int> (3)
62              Number of exclusions
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64       -[no]H14 (yes)
65              Use 3rd neighbour interactions for hydrogen atoms
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67       -[no]alldih (no)
68              Generate all proper dihedrals
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70       -[no]remdih (no)
71              Remove dihedrals on the same bond as an improper
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73       -[no]pairs (yes)
74              Output 1-4 interactions (pairs) in topology file
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76       -name <string> (ICE)
77              Name of your molecule
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79       -[no]pbc (yes)
80              Use periodic boundary conditions.
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82       -[no]pdbq (no)
83              Use the B-factor supplied in a .pdb file for the atomic charges
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85       -[no]param (yes)
86              Print parameters in the output
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88       -[no]round (yes)
89              Round off measured values
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91       -kb <real> (400000)
92              Bonded force constant (kJ/mol/nm^2)
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94       -kt <real> (400)
95              Angle force constant (kJ/mol/rad^2)
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97       -kp <real> (5)
98              Dihedral angle force constant (kJ/mol/rad^2)
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KNOWN ISSUES

101       • The atom type selection is primitive. Virtually no chemical knowledge
102         is used
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104       • Periodic boundary conditions screw up the bonding
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106       • No improper dihedrals are generated
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108       • The   atoms  to  atomtype  translation  table  is  incomplete  (atom‐
109         name2type.n2t file in
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111       • the data directory). Please extend it and send the  results  back  to
112         the GROMACS crew.
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SEE ALSO

115       gmx(1)
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117       More     information    about    GROMACS    is    available    at    <‐
118       http://www.gromacs.org/>.
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121       2022, GROMACS development team
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1262022.3                           Sep 02, 2022                     GMX-X2TOP(1)
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