Difference between revisions of "2013 AMBER Tutorial with UMP and OMP"

Revision as of 11:41, 25 March 2013

For additional Rizzo Lab tutorials see AMBER Tutorials.

In this tutorial, we will learn how to run a molecular dynamics simulation of a protein-ligand complex. We will then post-process that simulation by calculating structural fluctuations (with RMSD) and free energies of binding (MM-GBSA).

I. Introduction

AMBER

Amber - Assisted Model Building with Energy Refinement - is a suite of about multiple programs for perform macromolecular simulations. Amber11, the current version of Amber, includes newly released functionality such as PMEMD, particle mesh Ewald MD and soft-core Thermodynamics Integration MD. For the tutorial, we are using the newest version AMBER12.

The Amber 12 Manual is the primary resource to get started with Amber12. (Tip: Using Adobe Acrobat to view the file, you can simply search the document for keywords such as the name of a simulation parameter, which saves much time.) In addition, Amber Tools User's Manual serves as another reference while using Amber tools.

Here are some programs in Amber

1. LEaP: an preparing program for constructing new or modified systems in Amber. It consists of the functions of prep, link, edit, and parm for earlier version of Amber.
2. ANTECHAMBER: in additional to LEap, this main Antechamber suite program is for preparing input files other than standard nucleic acids and proteins.
3. SANDER: according to the Amber 12 manual, it is 'a basic energy minimizer and molecular dynamics program' that can be used to minimize, equilibrate and sample molecular conformations. And this is the program we mainly use in this tutorial to generate trajectory files of the molecular system.
4. PMEMD: version of SANDER that has improved parallel scaling property and optimized speed.
5. PTRAJ: an analysis program for processing trajectory files. One can use ptraj to rotate, translate the structures, evaluate geometrical features and so on.

There is a mailing list you could sign-up for, as an additional resource.

UMP and OMP

For information of the UMP-OMP system, see 2013 DOCK tutorial with Orotodine Monophosphate Decarboxylase.

Organizing Directories

While performing MD simulations, it is convenient to adopt a standard directory structure / naming scheme, so that files are easy to find / identify. For this tutorial, we will use something similar to the following:

~username/AMS536/AMBER-Tutorial/001.CHIMERA.MOL.PREP/  
                                002.ANTE.TLEAP/ 
                                003.SANDER/       
                                004.PTRAJ/
                                005.MMGBSA/

II. Structural Preparation

Preparation in Chimera

antechamber

parmchk

tleaP

Visualization in VMD

III. Simulation using sander

Minimization

Equilibration

Production

Running jobs on the queue

IV. Simulation Analysis

Ptraj

RMSD Plots

Measuring h-bond distances

MMGBSA Energy Calculation

Equations for analysis

Plotting Energy

V. Frequently Encountered Problems

Artem

Brian

He

Jiahui

Jiaye

Koushik

Natalie

Nikolay

Weiliang

Ye

Yuan

Zach