2012 AMBER Tutorial with Biotin and Streptavidin
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).
- 1 I. Introduction
- 2 II. Structural Preparation
- 3 III. Simulation using sander
- 4 IV. Simulation Analysis
- 5 V. Frequently Encountered Problems
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
- 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.
- ANTECHAMBER: in additional to LEap, this main Antechamber suite program is for preparing input files other than standard nucleic acids and proteins.
- 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.
- PMEMD: version of SANDER that has improved parallel scaling property and optimized speed.
- 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.
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
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.
To 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, we can use the which command, type:
which antechamber which parmchk which tleap
You should have results similar to this:
/nfs/user03/tbalius/amber10_ompi/bin/antechamber /nfs/user03/tbalius/amber10_ompi/bin/parmchk /nfs/user03/tbalius/amber10_ompi/bin/tleap
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:
ANTECHAMBER_BOND_TYPE.AC ATOMTYPE.INF 1DF8.lig.ante.prep ANTECHAMBER_BOND_TYPE.AC0 NEWPDB.PDB ANTECHAMBER_AC.AC ANTECHAMBER_PREP.AC PREP.INF ANTECHAMBER_AC.AC0 ANTECHAMBER_PREP.AC0
These files give detailed information of the ligand such as atom coordinates, bond angle, bond length, dihedral angles, etc. For example:
You can see this file contains information related to the ring system.
parmchk is another program included in the Antechamber package. After running antechamber, we run parmchk to check the parameters. If there are missing parameters after antechamber is finished, the frcmod template generated by parmchk will help us in generating the needed parameters:
parmchk -i 1DF8.lig.ante.prep -f prepi -o 1DF8.lig.ante.frcmod
Then open the output file 1DF8.lig.ante.frcmod, you will see something like this:
remark goes here MASS BOND ANGLE DIHE IMPROPER c3-o -c -o 1.1 180.0 2.0 General improper torsional angle (1 general atom type) n -n -c -o 10.5 180.0 2.0 General improper torsional angle (2 general atom types) NONBON
This means all the needed force field parameters are avalaible except there are two missing dihedral parameters, which were assigned a default value.