| Molecular Modeling Lab |
In this page you can find the Enhanced Sampling of Binding and Pocket Volume and Shape (EDES) tutorial. We will exploit enhanced-sampling molecular dynamics, namely metadynamics, to improve the sampling of bound-like (holo) conformations of a generic protein starting from its unbound
Prerequisites: * Server license is already installed and configured for the group. * User needs a personal account on the Schrödinger website for downloads and support. Download Schrodinger Suite 1. Create an Account on Schrödinger's
A very short guide for installing python packages (pymol in this example) as a non-privileged user, inside a (python) virtual environment created with conda (miniconda). 1. Set conda installation home (CHOME) in bash:
In this page you can find the Enhanced Sampling of Binding and Pocket Volume and Shape (EDES) tutorial. We will exploit enhanced-sampling molecular dynamics, namely metadynamics, to improve the sampling of bound-like (holo)
https://pubs.acs.org/doi/10.1021/acs.jcim.8b00730
Go to the THIRD part of the Tutorial Analyzing the metadynamics simulation In this section, we are going to evaluate the enhancement of "breathing motions" of the BS (in terms of RoG oscillations,
Go to the SECOND part of the Tutorial Go to the FOURTH part of the Tutorial Preparing the PLUMED input files In the previous section you edited the plumed-common.dat file containing the