Blog

In our previous tutorial, we saw step by step how one can externally parametrize a ligand and build a protein-ligand system topology for MD simulations with Gromacs. However, this method, although simple, can be quite tedious, especially if you have to parametrize a large number of systems with different ligands.... [Read More]

Working with metal-containing proteins is often very complicated, especially when no standard focefields are available for treating this specific type of metal and most importantly, the protein residues that are bonded to it. Luckily, a group of researchers form Italy published a modified AMBER forcefield that was optimized specifically for... [Read More]

Building a complex system containing a protein (especially a metalloprotein) that contains small molecules that act as co-factors and a docked ligand can be a very challenging procedure. In order to make things easier I created this tutorial using only free and open access resources, such as Antechamber, acpype and... [Read More]

MultiWfn is a very useful program for wavefunction analysis. You can use a .wfn or .wfx wavefunction file for plotting any occupied orbital, but for a more accurate LUMO (and any LUMO +n) the formatted checkpoint file is needed. I use Gaussian 16 for its generation. [Read More]

MultiWfn is a very useful program for wavefunction analysis. You will need a .wfn or .wfx file that is computed by your electronic structure calculation software (e.g. I am using gaussian to compute this file) and the MultiWfn software can help you extract various information that could be usefull for... [Read More]

Excited to share some incredible news! [Read More]