Topology File
From wiki.gromacs.org
There are three different types of topology files utilised by GROMACS.
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[edit] .top System Topology
The top file extension stands for topology. This topology file defines the entire systems 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 one 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.
[edit] .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 example,
[edit] .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.
