Generating topology of molecule for AMBER forcefield for GROMACS.

In this article, we will generate the topology of a small molecule for AMBER forcefield to be used in MD simulation using GROMACS.

For this, we will use the acpype Python script [1,2]. You can get this script from GitHub.  Let’s download some prerequisites before proceeding further.

$ sudo apt-get install -y openbabel python3-openbabel libarpack++2-dev libgfortran5

Generating topology

First, add missing hydrogens to the ligand using Openbabel.

$ obabel -ipdb ligand.pdb -h ligand.pdb -O ligand_with_H.pdb

Now, run the acpype script as shown below.

$ ./run_acpype.py -i ligand_with_H.pdb

It will create a new directory, called ligand_with_H.acpype. You can find the topology file for GROMACS inside this directory.

References

1. Sousa da Silva, A. W., & Vranken, W. F. (2012). ACPYPE-Antechamber python parser interface. BMC research notes, 5, 1-8.
2. Batista, P. R., Wilter, A., Durham, E. H., & Pascutti, P. G. (2006). Molecular dynamics simulations applied to the study of subtypes of HIV-1 protease common to Brazil, Africa, and Asia. Cell biochemistry and biophysics, 44, 395-404.