1GMX-X2TOP(1) GROMACS GMX-X2TOP(1)
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6 gmx-x2top - Generate a primitive topology from coordinates
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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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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.
20 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:
26 G53a5 GROMOS96 53a5 Forcefield (official distribution)
28 oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
30 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
34 interactive, 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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39 Options to specify input files:
40 -f [<.gro/.g96/…>] (conf.gro)
42 Structure file: gro g96 pdb brk ent esp tpr
43 Options to specify output files:
45 -o [<.top>] (out.top) (Optional)
47 Topology file
48 -r [<.rtp>] (out.rtp) (Optional)
50 Residue Type file used by pdb2gmx
51 Other options:
53 -ff <string> (oplsaa)
55 Force field for your simulation. Type “select” for interactive
56 selection.
57 -[no]v (no)
59 Generate verbose output in the top file.
60 -nexcl <int> (3)
62 Number of exclusions
63 -[no]H14 (yes)
65 Use 3rd neighbour interactions for hydrogen atoms
66 -[no]alldih (no)
68 Generate all proper dihedrals
69 -[no]remdih (no)
71 Remove dihedrals on the same bond as an improper
72 -[no]pairs (yes)
74 Output 1-4 interactions (pairs) in topology file
75 -name <string> (ICE)
77 Name of your molecule
78 -[no]pbc (yes)
80 Use periodic boundary conditions.
81 -[no]pdbq (no)
83 Use the B-factor supplied in a .pdb file for the atomic charges
84 -[no]param (yes)
86 Print parameters in the output
87 -[no]round (yes)
89 Round off measured values
90 -kb <real> (400000)
92 Bonded force constant (kJ/mol/nm^2)
93 -kt <real> (400)
95 Angle force constant (kJ/mol/rad^2)
96 -kp <real> (5)
98 Dihedral angle force constant (kJ/mol/rad^2)
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101 · The atom type selection is primitive. Virtually no chemical knowledge
102 is used
103 · Periodic boundary conditions screw up the bonding
105 · No improper dihedrals are generated
107 · The atoms to atomtype translation table is incomplete (atom‐
109 name2type.n2t file in the data directory). Please extend it and send
110 the results back to the GROMACS crew.
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113 gmx(1)
114 More information about GROMACS is available at <‐
116 http://www.gromacs.org/>.
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119 2019, GROMACS development team
1202019.4 Oct 02, 2019 GMX-X2TOP(1)