share/html/online/top.html

   1 <title>top file format</title>
   2 <body>
   3 <h1>top file format</h1>
   4 The top file extension stands for topology. It is an ascii file which is
   5 read by <a href="grompp.html">grompp</a> which processes it
   6 and creates a binary topology (<a href="tpb.html">tpb-file</a>).<br>
   7 A sample file is included below:
   8 <pre>
   9 ;
  10 ;       Example topology file
  11 ;
  12 [ defaults ]
  13 ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
  14   1             1               no              1.0     1.0
  15
  16 ; The force field files to be included
  17 #include "rt41c5.itp"
  18
  19 [ moleculetype ]
  20 ; name  nrexcl
  21 Urea         3
  22
  23 [ atoms ]
  24 ;   nr    type   resnr  residu    atom    cgnr  charge
  25      1       C       1    UREA      C1       1   0.683
  26      2       O       1    UREA      O2       1  -0.683
  27      3      NT       1    UREA      N3       2  -0.622
  28      4       H       1    UREA      H4       2   0.346
  29      5       H       1    UREA      H5       2   0.276
  30      6      NT       1    UREA      N6       3  -0.622
  31      7       H       1    UREA      H7       3   0.346
  32      8       H       1    UREA      H8       3   0.276
  33
  34 [ bonds ]
  35 ;  ai    aj funct           c0           c1
  36     3     4     1 1.000000e-01 3.744680e+05
  37     3     5     1 1.000000e-01 3.744680e+05
  38     6     7     1 1.000000e-01 3.744680e+05
  39     6     8     1 1.000000e-01 3.744680e+05
  40     1     2     1 1.230000e-01 5.020800e+05
  41     1     3     1 1.330000e-01 3.765600e+05
  42     1     6     1 1.330000e-01 3.765600e+05
  43
  44 [ pairs ]
  45 ;  ai    aj funct           c0           c1
  46     2     4     1 0.000000e+00 0.000000e+00
  47     2     5     1 0.000000e+00 0.000000e+00
  48     2     7     1 0.000000e+00 0.000000e+00
  49     2     8     1 0.000000e+00 0.000000e+00
  50     3     7     1 0.000000e+00 0.000000e+00
  51     3     8     1 0.000000e+00 0.000000e+00
  52     4     6     1 0.000000e+00 0.000000e+00
  53     5     6     1 0.000000e+00 0.000000e+00
  54
  55 [ angles ]
  56 ;  ai    aj    ak funct           c0           c1
  57     1     3     4     1 1.200000e+02 2.928800e+02
  58     1     3     5     1 1.200000e+02 2.928800e+02
  59     4     3     5     1 1.200000e+02 3.347200e+02
  60     1     6     7     1 1.200000e+02 2.928800e+02
  61     1     6     8     1 1.200000e+02 2.928800e+02
  62     7     6     8     1 1.200000e+02 3.347200e+02
  63     2     1     3     1 1.215000e+02 5.020800e+02
  64     2     1     6     1 1.215000e+02 5.020800e+02
  65     3     1     6     1 1.170000e+02 5.020800e+02
  66
  67 [ dihedrals ]
  68 ;  ai    aj    ak    al funct           c0           c1           c2
  69     2     1     3     4     1 1.800000e+02 3.347200e+01 2.000000e+00
  70     6     1     3     4     1 1.800000e+02 3.347200e+01 2.000000e+00
  71     2     1     3     5     1 1.800000e+02 3.347200e+01 2.000000e+00
  72     6     1     3     5     1 1.800000e+02 3.347200e+01 2.000000e+00
  73     2     1     6     7     1 1.800000e+02 3.347200e+01 2.000000e+00
  74     3     1     6     7     1 1.800000e+02 3.347200e+01 2.000000e+00
  75     2     1     6     8     1 1.800000e+02 3.347200e+01 2.000000e+00
  76     3     1     6     8     1 1.800000e+02 3.347200e+01 2.000000e+00
  77
  78 [ dihedrals ]
  79 ;  ai    aj    ak    al funct           c0           c1
  80     3     4     5     1     2 0.000000e+00 1.673600e+02
  81     6     7     8     1     2 0.000000e+00 1.673600e+02
  82     1     3     6     2     2 0.000000e+00 1.673600e+02
  83
  84 ; Include SPC water topology
  85 #include "spc.itp"
  86
  87 [ system ]
  88 Urea in Water
  89
  90 [ molecules ]
  91 Urea    1
  92 SOL     1000
  93 </pre>
  94 </body>