2013 AMBER Tutorial with UMP and OMP

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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 - 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.


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:


II. Structural Preparation

Preparation in Chimera

In this AMBER tutorial, we will use the same system with previous DOCK part. To begin with, we need three files under directory 001.CHIMERA.MOL.PREP.

Downloading the PDB file (1LOQ)

Since we need to edit the PDB before we use it in Chimera we should do this manually. Go to PDB homepage (http://www.rcsb.org/pdb/home/home.do ) enter the protein ID (1LOQ) in the search bar, click Download Files in the top-right of the webpage, then select PDB File (text). In the new window, save the file in Downloads.

Preparing the ligand and receptor in Chimera

In this section, we will create three new files and save them in the 001.CHIMERA.MOL.PREP/ folder:

 1LOQ.dockprep.mol2      (complete system with hydrogens and charges)
 1LOQ.receptor.noH.mol2  (the receptor alone, without hydrogens)
 1LOQ.ligand.mol2        (the ligand alone)

To prepare these files, first copy the original PDB file into the 00.files/ folder and open it with VIM ($ vim 1LOQ.pdb). Because the residue name of the ligand (U) will give us some problems when assigning charges, change the residue name "U" to "LIG" starting at line 2082. Here is an example command that will change all instances of " U" into "LIG", while preserving the correct spacing:

 %s/  U/LIG/gc

For this command, g is short for global and c is short for check with the user before making the change.

Next, open up the PDB file (1LOQ.pdb) in Chimera. To delete water molecules and other ligands, click Tools -> Structure Editing -> Dock Prep. Check all boxes and click Okay to the end. Alternatively, the waters can be deleted manually by choosing Select -> Residue -> HOH, then go to Actions -> Atoms/Bonds -> Delete. Hydrogen atoms can be added manually by choosing Tools -> Structure Editing -> Add H.

Next, to add charges to the ligand and receptor, go to Select -> Residue -> LIG, then go to Tools -> Structure Editing -> Add Charge. Choose AMBER ff99SB as the charge model, click Okay, and when prompted chose AM1-BCC charges for the ligand, and make sure the Net Charge is set to -1. (You must consider the chemistry of the ligand when assigning a charge state).

Finally, save this file as 1LOQ.dockprep.mol2.

Generating the final files

To create the receptor file with no hydrogen atoms: Open 1LOQ.dockprep.mol2, click Select -> Chemistry -> Element -> H, then chose Actions -> Atoms/Bonds -> Delete. Save the file as 1LOQ.receptor.noH.mol2.

To create the ligand file: Open 1LOQ.dockprep.mol2, click Select -> Residue -> LIG, then click Select -> Invert, then chose Actions -> Atoms/Bonds -> Delete. Save the file as 1LOQ.ligand.mol2.

An antechamber input file for the next step requires all the atom names to be unique and it only uses the first 3 characters as the name. So if we use 1LOQ.lig.chimera.mol2 as the input file, it will cause errors ("H102" and "H103" will have the same name "H10") We can use Vim to rename the hydrogens, or any other atom with 4 character name. Make these edits and save as 1LOQ.ligand.mol2




Visualization in VMD

III. Simulation using sander




Running jobs on the queue

IV. Simulation Analysis


RMSD Plots

Measuring h-bond distances

MM-GBSA Energy Calculation

Equations for analysis

Plotting Energy

V. Frequently Encountered Problems