docs/old-html/online/top.html

   1 <title>top file format</title>
   2 <H3>Description</H3>
   3 The top file extension stands for topology. It is an ascii file which is
   4 read by <a href="../programs/gmx-grompp.html">gmx grompp</a> which processes it
   5 and creates a binary topology (<a href="tpb.html">.tpb file</a>).<br>
   6 A sample file is included below:
   7 <pre>
   8 ;
   9 ;       Example topology file
  10 ;
  11 [ defaults ]
  12 ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
  13   1             1               no              1.0     1.0
  14
  15 ; The force field files to be included
  16 #include "rt41c5.itp"
  17
  18 [ moleculetype ]
  19 ; name  nrexcl
  20 Urea         3
  21
  22 [ atoms ]
  23 ;   nr    type   resnr  residu    atom    cgnr  charge
  24      1       C       1    UREA      C1       1   0.683
  25      2       O       1    UREA      O2       1  -0.683
  26      3      NT       1    UREA      N3       2  -0.622
  27      4       H       1    UREA      H4       2   0.346
  28      5       H       1    UREA      H5       2   0.276
  29      6      NT       1    UREA      N6       3  -0.622
  30      7       H       1    UREA      H7       3   0.346
  31      8       H       1    UREA      H8       3   0.276
  32
  33 [ bonds ]
  34 ;  ai    aj funct           c0           c1
  35     3     4     1 1.000000e-01 3.744680e+05
  36     3     5     1 1.000000e-01 3.744680e+05
  37     6     7     1 1.000000e-01 3.744680e+05
  38     6     8     1 1.000000e-01 3.744680e+05
  39     1     2     1 1.230000e-01 5.020800e+05
  40     1     3     1 1.330000e-01 3.765600e+05
  41     1     6     1 1.330000e-01 3.765600e+05
  42
  43 [ pairs ]
  44 ;  ai    aj funct           c0           c1
  45     2     4     1 0.000000e+00 0.000000e+00
  46     2     5     1 0.000000e+00 0.000000e+00
  47     2     7     1 0.000000e+00 0.000000e+00
  48     2     8     1 0.000000e+00 0.000000e+00
  49     3     7     1 0.000000e+00 0.000000e+00
  50     3     8     1 0.000000e+00 0.000000e+00
  51     4     6     1 0.000000e+00 0.000000e+00
  52     5     6     1 0.000000e+00 0.000000e+00
  53
  54 [ angles ]
  55 ;  ai    aj    ak funct           c0           c1
  56     1     3     4     1 1.200000e+02 2.928800e+02
  57     1     3     5     1 1.200000e+02 2.928800e+02
  58     4     3     5     1 1.200000e+02 3.347200e+02
  59     1     6     7     1 1.200000e+02 2.928800e+02
  60     1     6     8     1 1.200000e+02 2.928800e+02
  61     7     6     8     1 1.200000e+02 3.347200e+02
  62     2     1     3     1 1.215000e+02 5.020800e+02
  63     2     1     6     1 1.215000e+02 5.020800e+02
  64     3     1     6     1 1.170000e+02 5.020800e+02
  65
  66 [ dihedrals ]
  67 ;  ai    aj    ak    al funct           c0           c1           c2
  68     2     1     3     4     1 1.800000e+02 3.347200e+01 2.000000e+00
  69     6     1     3     4     1 1.800000e+02 3.347200e+01 2.000000e+00
  70     2     1     3     5     1 1.800000e+02 3.347200e+01 2.000000e+00
  71     6     1     3     5     1 1.800000e+02 3.347200e+01 2.000000e+00
  72     2     1     6     7     1 1.800000e+02 3.347200e+01 2.000000e+00
  73     3     1     6     7     1 1.800000e+02 3.347200e+01 2.000000e+00
  74     2     1     6     8     1 1.800000e+02 3.347200e+01 2.000000e+00
  75     3     1     6     8     1 1.800000e+02 3.347200e+01 2.000000e+00
  76
  77 [ dihedrals ]
  78 ;  ai    aj    ak    al funct           c0           c1
  79     3     4     5     1     2 0.000000e+00 1.673600e+02
  80     6     7     8     1     2 0.000000e+00 1.673600e+02
  81     1     3     6     2     2 0.000000e+00 1.673600e+02
  82
  83 ; Include SPC water topology
  84 #include "spc.itp"
  85
  86 [ system ]
  87 Urea in Water
  88
  89 [ molecules ]
  90 Urea    1
  91 SOL     1000
  92 </pre>