docs/old-html/online/rtp.html

   1 <title>rtp file format</title>
   2 <H3>Description</H3>
   3 The rtp file extension stands for residue toplogy.
   4 Such a file is needed by <a href="../programs/gmx-pdb2gmx.html">gmx pdb2gmx</a>
   5 to make a GROMACS topology for a protein contained in a <tt>.pdb</tt>
   6 file. The file contains the default interaction type for the 4 bonded
   7 interactions and residue entries, which consist of atoms and
   8 optionally bonds, angles dihedrals and impropers.
   9 Parameters can be added to bonds, angles, dihedrals and impropers,
  10 these parameters override the standard parameters
  11 in the <a href="itp.html"><tt>.itp</tt></a> files.
  12 This should only be used in special cases.
  13 Instead of parameters a string can be added for each bonded interaction,
  14 the string is copied to the <a href="top.html"><tt>.top</tt></a> file,
  15 this is used for the GROMOS96 forcefield.
  16 <p>
  17 <a href="../programs/gmx-pdb2gmx.html">gmx pdb2gmx</a>
  18 automatically generates all angles,
  19 this means that the <tt>[angles]</tt> field is only
  20 useful for overriding <a href="itp.html"><tt>.itp</tt></a> parameters.
  21 <p>
  22 <a href="../programs/gmx-pdb2gmx.html">gmx pdb2gmx</a>
  23 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 href="../programs/gmx-pdb2gmx.html">gmx pdb2gmx</a>
  30 sets the number exclusions to 3, which
  31 means that interactions between atoms connected by at most 3 bonds are
  32 excluded. Pair interactions are generated for all pairs of atoms which are
  33 seperated by 3 bonds (except pairs of hydrogens).
  34 When more interactions need to be excluded, or some pair interactions should
  35 not be generated, an <tt>[exclusions]</tt> field can be added, followed by
  36 pairs of atom names on seperate lines. All non-bonded and pair interactions
  37 between these atoms will be excluded.
  38 <p>
  39 A sample is included below.
  40
  41
  42 <PRE>
  43 [ bondedtypes ]  ; mandatory
  44 ; bonds  angles  dihedrals  impropers
  45      1       1          1          2  ; mandatory
  46
  47 [ GLY ]  ; mandatory
  48
  49  [ atoms ]  ; mandatory
  50 ; name  type  charge  chargegroup
  51      N     N  -0.280     0
  52      H     H   0.280     0
  53     CA   CH2   0.000     1
  54      C     C   0.380     2
  55      O     O  -0.380     2
  56
  57  [ bonds ]  ; optional
  58 ;atom1 atom2      b0      kb
  59      N     H
  60      N    CA
  61     CA     C
  62      C     O
  63     -C     N
  64
  65  [ exclusions ]  ; optional
  66 ;atom1 atom2
  67
  68  [ angles ]  ; optional
  69 ;atom1 atom2 atom3    th0    cth
  70
  71  [ dihedrals ]  ; optional
  72 ;atom1 atom2 atom3 atom4   phi0     cp   mult
  73
  74  [ impropers ]  ; optional
  75 ;atom1 atom2 atom3 atom4     q0     cq
  76      N    -C    CA     H
  77     -C   -CA     N    -O
  78
  79
  80 [ ZN ]
  81  [ atoms ]
  82     ZN    ZN   2.000     0
  83 </PRE>