18. VEGA ZZ tutorials
- How to build a small molecule
This tutorial explains how to build a small molecule (e.g. a ligand) by using
different editors included in VEGA ZZ and how to perform a systematic
conformational search (grid scan) in order to find the best conformer.
- Energy minimization of a protein with NAMD
VEGA ZZ allows to prepare the input files for NAMD in easy way without the
use of complex software to generate the topology. In this tutorial is explained
step-by-step how to perform a simple conjugate gradients energy minimization
of the crambin crystallographic structure with and without constraints.
- Molecular dynamics of a non-peptic molecule with
This tutorial explains how to perform the molecular dynamics simulation of the
ibuprofen - water system with NAMD. The ibuprofen is a non-peptidic molecule and
so some potential parameters are missing in the standard CHARMM 22 force field.
You can learn how to fix the missing force field parameters and how to run
NAMD without the VEGA ZZ graphic interface.
- Molecular docking with VEGA ZZ and Fred
VEGA ZZ, Fred and NAMD are very efficient tools to perform a complete
molecular docking analysis. This tutorial explains in details how was
performed the docking between the farnesyltransferase enzyme (FTase) and a set
of inhibitors as published in the paper: Bolchi C., Pallavicini M., Rusconi
C., Diomede L., Ferri N., Corsini A., Fumagalli L., Pedretti A., Vistoli G.,
Valoti E., "Peptidomimetic inhibitors of farnesyltransferase with high in
vitro activity and significant cellular potency", Bioorg. Med. Chem. Lett.,
17(22), 6192-6 (2007).
- Virtual screening with VEGA ZZ and GriDock
The structure-based virtual screening is a very interesting approach
to find new hit compounds from a database of 3D molecules. In this tutorial,
it's explained how to prepare the input files required by GriDock to find
potential inhibitors of the HIV-1 protease.