Welcome to the Molecular Graphics and Computation Facility


Facility Director, Dr. Kathy Durkin durkin@berkeley.edu

Facility Scientist, Dr. Dave Small mgcf@berkeley.edu
(Dr. Yinka Olatunji-Ojo recently took a new job in the south bay!)

Tutorials and related documents. We have copies in the lab for you, but here are google doc or html versions.

Computational Methods Summary

Linux - Basic Commands

Intro to Materials Studio

Intro to Cambridge Structural Database

Intro to Gaussian16

Gaussian SN2 Transition State

Gaussian Spin Polarization

Gaussian TDDFT - Gas Phase

Gaussian TDDFT - Solution Phase

Maestro and related programs:

Maestro Shortcuts

Intro to Molecular Mechanics in Macromodel + Maestro: Conformers of Lactose

Glide + Maestro - Intro to Docking

Desmond + Maestro - Intro to Molecular Dynamics

Jaguar + Maestro - DFT and Electrostatic Potential Surface

Other Tutorials - PDFS

Other Programs:

QChem Primer

Sample files for many tutorials are here.