rtp file format

Main Table of Contents VERSION 5.0.7


The rtp file extension stands for residue toplogy. Such a file is needed by gmx pdb2gmx to make a GROMACS topology for a protein contained in a .pdb file. The file contains the default interaction type for the 4 bonded interactions and residue entries, which consist of atoms and optionally bonds, angles dihedrals and impropers. Parameters can be added to bonds, angles, dihedrals and impropers, these parameters override the standard parameters in the .itp files. This should only be used in special cases. Instead of parameters a string can be added for each bonded interaction, the string is copied to the .top file, this is used for the GROMOS96 forcefield.

gmx pdb2gmx automatically generates all angles, this means that the [angles] field is only useful for overriding .itp parameters.

gmx pdb2gmx automatically generates one proper dihedral for every rotatable bond, preferably on heavy atoms. When the [dihedrals] field is used, no other dihedrals will be generated for the bonds corresponding to the specified dihedrals. It is possible to put more than one dihedral on a rotatable bond.

gmx pdb2gmx sets the number exclusions to 3, which means that interactions between atoms connected by at most 3 bonds are excluded. Pair interactions are generated for all pairs of atoms which are seperated by 3 bonds (except pairs of hydrogens). When more interactions need to be excluded, or some pair interactions should not be generated, an [exclusions] field can be added, followed by pairs of atom names on seperate lines. All non-bonded and pair interactions between these atoms will be excluded.

A sample is included below.

[ bondedtypes ]  ; mandatory
; bonds  angles  dihedrals  impropers
     1       1          1          2  ; mandatory

[ GLY ]  ; mandatory

 [ atoms ]  ; mandatory 
; name  type  charge  chargegroup       
     N     N  -0.280     0
     H     H   0.280     0
    CA   CH2   0.000     1
     C     C   0.380     2
     O     O  -0.380     2

 [ bonds ]  ; optional
;atom1 atom2      b0      kb
     N     H
     N    CA
    CA     C
     C     O
    -C     N

 [ exclusions ]  ; optional
;atom1 atom2

 [ angles ]  ; optional
;atom1 atom2 atom3    th0    cth

 [ dihedrals ]  ; optional
;atom1 atom2 atom3 atom4   phi0     cp   mult

 [ impropers ]  ; optional
;atom1 atom2 atom3 atom4     q0     cq
     N    -C    CA     H
    -C   -CA     N    -O

[ ZN ]
 [ atoms ]
    ZN    ZN   2.000     0