share/html/online/rtp.html

   1 <title>rtp file format</title>
   2 <body>
   3 <h1>rtp file format</h1>
   4 <h2>Description</h2>
   5 The rtp file extension stands for residue toplogy.
   6 Such a file is needed by <a href="pdb2gmx.html">pdb2gmx</a>
   7 to make a GROMACS topology for a protein contained in a <tt>.pdb</tt>
   8 file. The file contains the default interaction type for the 4 bonded
   9 interactions and residue entries, which consist of atoms and
  10 optionally bonds, angles dihedrals and impropers.
  11 Parameters can be added to bonds, angles, dihedrals and impropers,
  12 these parameters override the standard parameters
  13 in the <a href="itp.html"><tt>.itp</tt></a> files.
  14 This should only be used in special cases.
  15 Instead of parameters a string can be added for each bonded interaction,
  16 the string is copied to the <a href="top.html"><tt>.top</tt></a> file,
  17 this is used for the GROMOS96 forcefield.
  18 <p>
  19 <a href="pdb2gmx.html">pdb2gmx</a> automatically generates all angles,
  20 this means that the <tt>[angles]</tt> field is only
  21 useful for overriding <a href="itp.html"><tt>.itp</tt></a> parameters.
  22 <p>
  23 <a href="pdb2gmx.html">pdb2gmx</a> automatically generates one proper
  24 dihedral for every rotatable bond, preferably on heavy atoms.
  25 When the <tt>[dihedrals]</tt> field is used, no other dihedrals will
  26 be generated for the bonds corresponding to the specified dihedrals.
  27 It is possible to put more than one dihedral on a rotatable bond.
  28 <p>
  29 A sample is included below.
  30
  31
  32 <PRE>
  33 [ bondedtypes ]  ; mandatory
  34 ; bonds  angles  dihedrals  impropers
  35      1       1          1          2  ; mandatory
  36
  37 [ GLY ]  ; mandatory
  38
  39  [ atoms ]  ; mandatory
  40 ; name  type  charge  chargegroup
  41      N     N  -0.280     0
  42      H     H   0.280     0
  43     CA   CH2   0.000     1
  44      C     C   0.380     2
  45      O     O  -0.380     2
  46
  47  [ bonds ]  ; optional
  48 ;atom1 atom2      b0      kb
  49      N     H
  50      N    CA
  51     CA     C
  52      C     O
  53     -C     N
  54
  55  [ angles ]  ; optional
  56 ;atom1 atom2 atom3    th0    cth
  57
  58  [ dihedrals ]  ; optional
  59 ;atom1 atom2 atom3 atom4   phi0     cp   mult
  60
  61  [ impropers ]  ; optional
  62 ;atom1 atom2 atom3 atom4     q0     cq
  63      N    -C    CA     H
  64     -C   -CA     N    -O
  65
  66
  67 [ ZN ]
  68  [ atoms ]
  69     ZN    ZN   2.000     0
  70 </PRE>
  71 </body>