2012 AMBER Tutorial with Biotin and Streptavidin

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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 an older version which is AMBER10.

The Amber 10 Manual is the primary resource to get started with Amber10. (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. You can also read the manual for Amber11 on Amber11 and AmberTools Users' Manuals

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 10 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.

Biotin and Streptavidin

For information of the Biotin and Streptavidin system, see 2012 DOCK tutorial with Streptavidin.

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. Chimera can directly get the structure by its PDB ID 1DF8. To begin with, we need three files under directory 001.CHIMERA.MOL.PREP.

1. To lower computational cost and make the system clear, we remove chain B of the dimer. Select - chain - B, Action - Atoms/Bonds - delete
2. Remove the water molecules. Select - residue - HOH, Action - Atoms/Bonds - delete

Then we separate the receiver and its ligand.

Select the ligand and delete it. Select - Residue - BTN, Action - Atoms/Bonds - delete

1. Select the protein and delete it. Select - Residue - BTN, Select - Invert, Action - Atoms/Bonds - delete
2. Use Dock Prep to add hydrogens and charges(AM1-BCC) to the ligand. Tools - Structure Editing - Dock Prep


A antechamber input file requires all the atom names to be unique and it only uses the first 3 characters as the name. So if we use 1DF8.lig.chimera.mol2 as the input file, it will cause errors("H102" and "H103" will have the same name "H10").

    14 O3         26.9770   10.6020   12.2050 O.2       1 BTN201     -0.6531
    15 N2         28.6480   12.1210   11.8210 N.pl3     1 BTN201     -0.4789
    16 C4         28.9670   13.2060   10.9010 C.3       1 BTN201      0.0816
    17 H102       32.0358   17.4077   15.9597 H         1 BTN201      0.0272
    18 H103       30.6885   18.0473   15.0102 H         1 BTN201      0.0219
    19 H92        30.5603   15.6243   15.3130 H         1 BTN201     -0.0094
    20 H93        32.1288   15.4384   14.4982 H         1 BTN201      0.0384
    21 H82        29.6624   16.7125   13.2433 H         1 BTN201      0.0275

We need to manually rename the atoms. One way is to use the first column numbers to be the atom names. If you are using Vim, the visual block mode can help by selecting a rectangular section of text. We rename the atoms and save the file as 1DF8.lig.mol2 under directory 001.CHIMERA.MOL.PREP.

    14 O14       26.9770   10.6020   12.2050 O.2       1 BTN201     -0.6531
    15 N15       28.6480   12.1210   11.8210 N.pl3     1 BTN201     -0.4789
    16 C16       28.9670   13.2060   10.9010 C.3       1 BTN201      0.0816
    17 H17       32.0358   17.4077   15.9597 H         1 BTN201      0.0272
    18 H18       30.6885   18.0473   15.0102 H         1 BTN201      0.0219
    19 H19       30.5603   15.6243   15.3130 H         1 BTN201     -0.0094
    20 H20       32.1288   15.4384   14.4982 H         1 BTN201      0.0384
    21 H21       29.6624   16.7125   13.2433 H         1 BTN201      0.0275


To begin with, go to 002.ANTE.TLEAP directory. Make sure we have access to the three programs that we want to run (antechamber, tleap and parmchk) and we are using the correct version of amber by using the which command, type:

which antechamber
which parmchk
which tleap

You should have results similar to this:


Please note that you need to be in the tcsh shell for running the which command shown above. Also, if you are using a different version of amber, you might want to change to the correct version by editing the .cshrc file and source it.

Copy parameters of ions to your working directory from the following resource:

scp -r ~lingling/AMS536/AMBER_Tutorial/002.ANTE.TLEAP/rizzo_amber7.ionparms .

Antechamber is a set of tools to generate files for organic molecules, which can then be read into LEaP. The antechamber program itself is the main program of Antechamber. It can perform many file conversions, and can also assign atomic charges and atom types. In this tutorial, we use antechamber to convert our input mol2 file into files ready for LEaP. In the command line, type:

antechamber -i ../001.CHIMERA.MOL.PREP/1DF8.lig.mol2 -fi mol2 -o 1DF8.lig.ante.pdb -fo pdb

-i input file name; -fi input file format; -o output file name; -fo output file format. You will have an output file:


Similarly, we can use antechamber to change the fomat of 1DF8.lig.mol2 file to prep file:

antechamber -i ../001.CHIMERA.MOL.PREP/1DF8.lig.mol2 -fi mol2 -o 1DF8.lig.ante.prep -fo prepi

You will get a set of output files:

1DF8.lig.ante.prep         ANTECHAMBER_BOND_TYPE.AC0  NEWPDB.PDB

Visualization in VMD

III. Simulation using sander

Minimization and equilibration


IV. Simulation Analysis


MMGBSA Energy Calculation

V. Frequently Encountered Problems