Step Two: Examine the Topology
Let's look at what is in the output topology (topol.top). Again, using a plain text editor, inspect its contents. After several comment lines (preceded by ;), you will find the following:
This line calls the parameters within the OPLS-AA force field. It is at the beginning of the file, indicating that all subsequent parameters are derived from this force field. The next important line is
; Name nrexcl Protein_A 3
The name "Protein_A" defines the molecule name, based on the fact that the protein was labeled as chain A in the PDB file. There are 3 exclusions for bonded neighbors. More information on exclusions can be found in the GROMACS manual; a discussion of this information is beyond the scope of this tutorial.
The next section defines the
[ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 1 LYS rtp LYSH q +2.0 1 opls_287 1 LYS N 1 -0.3 14.0067 ; qtot -0.3 2 opls_290 1 LYS H1 1 0.33 1.008 ; qtot 0.03 3 opls_290 1 LYS H2 1 0.33 1.008 ; qtot 0.36 4 opls_290 1 LYS H3 1 0.33 1.008 ; qtot 0.69 5 opls_293B 1 LYS CA 1 0.25 12.011 ; qtot 0.94 6 opls_140 1 LYS HA 1 0.06 1.008 ; qtot 1
The interpretation of this information is as follows:
Subsequent sections include
The remainder of the file involves defining a few other useful/necessary topologies, starting with position restraints. The "posre.itp" file was generated by pdb2gmx; it defines a force constant used to keep atoms in place during equilibration (more on this later).
; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif
This ends the "Protein_A" moleculetype definition. The remainder of the topology file is dedicated to defining other molecules and providing system-level descriptions. The next moleculetype (by default) is the solvent, in this case SPC/E water. Other typical choices for water include SPC, TIP3P, and TIP4P. We chose this by passing "-water spce" to pdb2gmx. For an excellent summary of the many different water models, click here, but be aware that not all of these models are present within GROMACS.
; Include water topology #include "oplsaa.ff/spce.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif
As you can see, water can also be position-restrained, using a force constant (kpr) of 1000 kJ mol-1 nm-2.
Ion parameters are included next:
; Include generic topology for ions #include "oplsaa.ff/ions.itp"
Finally come system-level definitions. The
[ system ] ; Name LYSOZYME [ molecules ] ; Compound #mols Protein_A 1
A few key notes about the
If you fail to satisfy these concrete requirements at any time, you will get fatal errors from grompp (discussed later) about mismatched names, molecules not being found, or a number of others.
Now that we have examined the contents of a topology file, we can continue building our system.
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