Topology File

.top System Topology

The .top file extension stands for topology. This topology file defines the entire system topology, either directly or by including .itp files (using the include file mechanism). It is an ASCII file which is read by grompp, which processes it and creates a binary topology (.tpr).

You can produce a .top file either by using pdb2gmx on a coordinate file (if the residues are present in your force field's .rtp file), or by hand in a text editor. If you already have an .itp file for every molecule in your system, you do not need to use pdb2gmx to generate your .top file - just use the include file mechanism to include the files, following an existing .top file and/or the GROMACS Manual for the syntax.

• top file format

.itp Include Topology

This file format is used to define individual (or multiple) components of a topology as a separate file. This is particularly of use if there is a molecule that is used frequently. The file contains only the information for the particular molecule.

These .itp files are then included (using the include file mechanism) within the .top file to define the entire system's topology. Note that an .itp file will be specific to a given force field, and will only function when included by a .top file that has previously included the .itp files for that force field. Appropriate use of the #define and #ifdef mechanisms can permit the same .itp file to work with multiple force fields, e.g. share/top/water.itp.

If you already have a suitable .itp file for a molecule, then you do not need to run pdb2gmx on it.

See, for example, itp file format, or the wiki entry for .itp files.

An .itp file is also used for defining atom types and other data for individual force fields. These need to be included (with #include) before any of your [ molecule ] sections - that is, before any #include "file.itp" constructs for individual molecules. It is normally wrong to want more than one such force field file, and this will usually provoke an error from grompp.

.rtp Residue Topology

The .rtp file extension stands for residue topology. Such a file is needed by 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 improper dihedrals. 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.

One point that is not made clearly in the manual is how to specify the connectivity between residues. This mechanism was derived from protein connectivity, and relying on the existence in each residue of atoms with the same names, i.e. the protein backbone atoms. The [ bonds ] section in the example in section 5.6.1 of the manual defines a bond between -C and N. This refers to the C atom in the previous residue. Similarly, one might use a +N prefix to refer to the N atom in the following residue.  Such connectivity can be used for other polymeric materials. It does not generalize readily to branched polymers (including, for example, disulfide-bridged proteins), but the specbond.dat mechanism exists to treat such cases.

• .rtp file format, GROMACS Manual