In a lot of scientific papers visualization of surface charges or surface electrostatics is a common feature for the interpretation of protein-protein, protein-ligand interactions. However, in many cases the surface electrostatics are calculated at one pH value, because to calculate more pH values is quite time intensity. Therefore, the program…

Cyclic voltamograms (CV) are mostly copied to text files by simply clicking copy&paste, which is a easy way to get the data out of the program for further processing them in Microsoft Excel. However, most of the time the data are in the format of a first column, containing the…

To generate a charge-based surface model of your protein, three different programs are needed: 1) pdb2pqr, which calculates, based on the pH given, the protonation state of amino acids (mainly histidines, aspartic acid, glutamic acid, lysine and arginine) 2) APBS, which calculates electrostatics of the protein and 3) PyMol, which…

GROMOS is a software package to setup and run Molecular Dynamics Simulations. Gromos is more known for its force fields, than for running simulations with it. Therefore, this guide should help you to install GROMOS and use it to setup your simulation with Gromos force fields. …

Installing pre-compiled APBS for electrostatic surface and PDB2PQR for protonation state calculations on Ubuntu/MacOsX How to get APBS and PDB2PQR running ABPS can be downloaded from the Github or Sourceforge repositories as pre-compiled binaries. However, after downloading the packages some additional things such as PATHs have to be adjusted to get the executable running. This article should…

This article should give a short overview of how to adjust the data usage while participating in a Zoom meeting. View settings and window sizes need different amounts of data. …

“ProtParam” is a tool available as web service for calculation of Protein parameters, such as Molecular weight, Extinction coefficient, … However, the usage via the webserver is not very handy if many sequences have to be processed. …

WSL under Windows10 First enable WSL under Windows10 WSL Normally you now have WSL 1 installed, which is completely OK for Gromacs, however to use for instance xmgrace you need a GUI (graphical user interface), therefore WSL 2 is necessary. WSL 2 can additionally be installed under Windows10. (WSL 1 & 2) After…