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   4 <h2>rtp file format</h2>
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   8 <TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
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  10 <TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
  11 <H3>Description</H3>
  12 The rtp file extension stands for residue toplogy.
  13 Such a file is needed by <a href="pdb2gmx.html">pdb2gmx</a>
  14 to make a GROMACS topology for a protein contained in a <tt>.pdb</tt>
  15 file. The file contains the default interaction type for the 4 bonded
  16 interactions and residue entries, which consist of atoms and
  17 optionally bonds, angles dihedrals and impropers.
  18 Parameters can be added to bonds, angles, dihedrals and impropers,
  19 these parameters override the standard parameters
  20 in the <a href="itp.html"><tt>.itp</tt></a> files.
  21 This should only be used in special cases.
  22 Instead of parameters a string can be added for each bonded interaction,
  23 the string is copied to the <a href="top.html"><tt>.top</tt></a> file,
  24 this is used for the GROMOS96 forcefield.
  25 <p>
  26 <a href="pdb2gmx.html">pdb2gmx</a> automatically generates all angles,
  27 this means that the <tt>[angles]</tt> field is only
  28 useful for overriding <a href="itp.html"><tt>.itp</tt></a> parameters.
  29 <p>
  30 <a href="pdb2gmx.html">pdb2gmx</a> automatically generates one proper
  31 dihedral for every rotatable bond, preferably on heavy atoms.
  32 When the <tt>[dihedrals]</tt> field is used, no other dihedrals will
  33 be generated for the bonds corresponding to the specified dihedrals.
  34 It is possible to put more than one dihedral on a rotatable bond.
  35 <p>
  36 <a href="pdb2gmx.html">pdb2gmx</a> sets the number exclusions to 3, which
  37 means that interactions between atoms connected by at most 3 bonds are
  38 excluded. Pair interactions are generated for all pairs of atoms which are
  39 seperated by 3 bonds (except pairs of hydrogens).
  40 When more interactions need to be excluded, or some pair interactions should
  41 not be generated, an <tt>[exclusions]</tt> field can be added, followed by
  42 pairs of atom names on seperate lines. All non-bonded and pair interactions
  43 between these atoms will be excluded.
  44 <p>
  45 A sample is included below.
  46
  47
  48 <PRE>
  49 [ bondedtypes ]  ; mandatory
  50 ; bonds  angles  dihedrals  impropers
  51      1       1          1          2  ; mandatory
  52
  53 [ GLY ]  ; mandatory
  54
  55  [ atoms ]  ; mandatory
  56 ; name  type  charge  chargegroup
  57      N     N  -0.280     0
  58      H     H   0.280     0
  59     CA   CH2   0.000     1
  60      C     C   0.380     2
  61      O     O  -0.380     2
  62
  63  [ bonds ]  ; optional
  64 ;atom1 atom2      b0      kb
  65      N     H
  66      N    CA
  67     CA     C
  68      C     O
  69     -C     N
  70
  71  [ exclusions ]  ; optional
  72 ;atom1 atom2
  73
  74  [ angles ]  ; optional
  75 ;atom1 atom2 atom3    th0    cth
  76
  77  [ dihedrals ]  ; optional
  78 ;atom1 atom2 atom3 atom4   phi0     cp   mult
  79
  80  [ impropers ]  ; optional
  81 ;atom1 atom2 atom3 atom4     q0     cq
  82      N    -C    CA     H
  83     -C   -CA     N    -O
  84
  85
  86 [ ZN ]
  87  [ atoms ]
  88     ZN    ZN   2.000     0
  89 </PRE>
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