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First Molecular Dynamic Simulation
Step-2. Genarating Topology

Pietro Buffa

If the PDB file is ready you can input it into the first GROMACS tool: pdb2gmx. The goal of this program is to generate the following three files:

1) A Topology file (topol.top) of the molecule
2) A Position Restraint file (posre.itp) which defines the force used to keep the heavy atoms in place during equilibration step
3) A Post-processed Structure file (x-processed.gro)

The topology file (topol.top by default), contains all the necessary information to define the molecule before MD. It includes bounded parameters (bonds, angles, dihedrals) as well as nonbonded parameters (atom tipes, atomic weight, charges).

Execute the program using this command to the prompt:

> pdb2gmx -f 1AKI.pdb -o 1AKI-processed.gro -water spce

The structure will be processed and now you have to choose a specific Force Field (FF):

Select the Force Field:
0: GROMOS96 43a1 force field
1: GROMOS96 43a2 force field (improved alkane dihedrals)
2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
6: [DEPRECATED] Gromacs force field (see manual)
7: [DEPRECATED] Gromacs force field with hydrogens for NMR
8: Encad all-atom force field, using scaled-down vacuum charges
9: Encad all-atom force field, using full solvent charges

This is a really important choice because the FF contains the information that will be written into the topology file. You should read more information about each FF in order to apply the best one to your system. For this tutorial we will use the all-atom OPLS force field so, type 5 followed by "enter". There are many other options that can be passed to pdb2gmx so, take a look at these information using the following command:

> pdb2gmx -h

Please pay attention to the output of pdb2gmx because it told us that our protein has a net charge of +8e (based on its amino acid composition). This information will be really important in the Step-4 when you will have to add specific positive or negative ions in order to neutralize the system.

If you look at the topology file (topol.top) using a text editor, after several comment lines, you can find the following scheme:

Topology file

where:

nr = atom number
type = atom type
resnr = amino acid residue number
residue = amino acid residue name
atom = atom name
cgnr = charge group number
charge = charge for single atom
mass = mass for single atom
typeB, chargeB, massB = used for free energy perturbation

The rest sections of this file are quite self-explanatory and include: position restraint information, water topology information, ions topology information and the system definitions.

The program that you used in this step can not generate topologies for arbitrary molecules. Generally proteins, nucleic acids and some cofactors like NAD(H) and ATP are defined by pre-existing force field but, for any other molecules, for example drugs, you have to generate a specific force field using other software packages before using pdb2gmx.

Now we can continue building our system.

Go to the Step-3.

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