How to generate topology from SMILES for MD Simulation?

If you need to generate the topology of molecules using their SMILES, a simple Python script is available.

A tool known as ACPYPE [1,2] is quite helpful in generating topologies for molecular dynamics (MD) simulation. It also allows generating of topology directly from SMILES of compounds. You can get this tool from GitHub. Here, we are not going into details of installation. There are several ways of installation mentioned on their GitHub page. Download it from git and ensure you have AmberTools and Openbabel installed on your system.

Generating topology using SMILES

You will find a Python script named ‘run_acpype.py‘ inside the ‘acpype‘ directory. Use this script to generate topology as shown below.

$ ./run_acpype.py -i <write_smiles_string_here>

For example, to generate topology for Butyl Ethylene,

$ ./run_acpype.py -i CCCCC=C

You can find the generated topology inside a newly created directory, called ‘smiles_molecule.acpype’.

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.