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’.
- Sousa da Silva, A. W., & Vranken, W. F. (2012). ACPYPE-Antechamber python parser interface. BMC research notes, 5, 1-8.
- 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.
Video Tutorial: Calculating binding pocket volume using PyVol plugin.
[Tutorial] Installing jdock on Ubuntu (Linux).
jdock is an extended version of idock . It has the same features as the idock along with some bug fixes. However, the binary name and the GitHub repository names are changed. We are installing jdock on Ubuntu (Linux).
How to upgrade cmake on Ubuntu (Linux)?
In bioinformatics, cmake is used to install multiple software including GROMACS, jdock, and so on. Here is a short tutorial on how to upgrade cmake on Ubuntu and get rid of the previous version. (more…)
How to install GMXPBSA on Ubuntu (Linux)?
[Tutorial] Installing Pyrx on Windows.
How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?
Compiling GROMACS  with GPU can be trivial. Previously, we have provided a few articles on the same. In this article, we will solve an error frequently occurring during GROMACS installation.
Installing Autodock4 on MacOS.
How to install Autodock4 on Ubuntu?
DS Visualizer: Uses & Applications
Protein structure & folding information exploited from remote homologs.
Remote homologs are similar protein structures that share similar functions, but there is no easily detectable sequence similarity in them. A new study has revealed that the protein folding information can be exploited from remote homologous structures. A new tool is developed to recognize such proteins and predict their structure and folding pathway. (more…)
Pathonoia- A new tool to detect pathogens in RNA-seq data.
Detecting viruses and bacteria in RNA-seq data with less false positive rate is a difficult task. A new tool is introduced to detect pathogens in RNA-seq data with high precision and recall known as Pathonoia .
AlphaFill- New algorithm to fill ligands in AlphaFold models.
AlphaFold is a popular artificial intelligence based protein prediction tool . Though it predicts good protein structures, it lacks the capability to predict the small molecules present in the structure such as ligands. For this purpose, AlphaFill is introduced by Hekkelman et al.,. (more…)
How to calculate binding pocket volume using PyVol plugin in PyMol?
How to generate electron density map using Pymol?
Installing PyVOL plugin in Pymol on Ubuntu (Linux).
How to execute matlab from terminal in Ubuntu (Linux)?
How to install Kpax on Ubuntu (Linux)?
Kpax is a bioinformatics program to search and align protein structures . It is currently available for Linux platforms only. In this article, we are going to install the latest version of Kpax (5.1.3) on Ubuntu (Linux). (more…)
How to run do_dssp command (mkdssp) in Gromacs 2022?
In the latest version of GROMACS (2022) , there are some issues regarding the gmx do_dssp command. Apparently, this command either does not run displaying a fatal error, or if it runs then it does not read any frame from MD simulation files. In this article, we are going to run the same command for GROMACS 2022. (more…)