Difference between revisions of "2013 AMBER Tutorial with UMP and OMP"
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===Visualization in VMD=== | ===Visualization in VMD=== | ||
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| + | Visualization is an important step in AMBER molecular dynamics simulation as it allows for the viewing of molecules and molecule movements within a specified field of view. Several files prepared in the previous two steps will be required for the visualization of the ligand and its movement in the protein binding pocket. The first step that must be completed is the copying of all necessary information from Seawulf to Herbie. | ||
| + | |||
| + | Before exiting Seawulf, you can type: | ||
| + | scp -r ~/AMS536/AMBER_Tutorial/002.ANTE.TLEAP username@herbie.mathlab.sunysb.edu:~/AMS536/AMBER_Tutorial/ | ||
| + | |||
| + | Then, when in Herbie, type the command '''vmd''' in any directory and the program VMD will open on the computer. In the "VMD Main" window, click '''File > New Molecule'''. Now in the new window titled "Molecule File Browser" a few files must be selected and loaded. To select and load a file follow these steps: | ||
| + | 1. Click '''Browse...''' and select the file that you desire. | ||
| + | 2. Click the down button in the "Determine file type:" field and select the proper file type. | ||
| + | 3. Click '''Load''' and view the molecule/system in the original "VMD 1.8.5 OpenGL Display" window. | ||
==III. Simulation using sander== | ==III. Simulation using sander== | ||
Revision as of 14:15, 27 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).
Contents
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
- 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 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.
- 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.
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
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 001.CHIMERA.MOL.PREP/ 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.
antechamber
The antechamber program itself is the main program of Antechamber package. In most of cases, one should use this program instead of a series of separated programs to do molecular format convertion, atom type assignment and charge generation etc. An antechamber input file requires all the atom names to be unique. So if we use 1LOQ.ligand.mol2 as the input file, it will cause errors. The program can only recognize atom names of 3 characters ( In this case, H5' and H5'' cannot be distinguished from each other. )
22 H5' 40.0697 36.0506 37.6716 H 1 LIG210 0.0761
23 H5 40.6060 37.0416 36.2883 H 1 LIG210 0.0349
24 H4' 38.2510 37.5673 38.1082 H 1 LIG210 0.0967
25 H3' 38.2723 38.5564 35.5613 H 1 LIG210 0.1052
26 H2' 40.3056 39.7322 35.6920 H 1 LIG210 0.1188
27 H1' 39.7587 40.5927 38.4795 H 1 LIG210 0.0753
28 H6 41.3847 41.7815 39.3543 H 1 LIG210 0.0322
29 H5 43.6843 42.3632 39.6188 H 1 LIG210 0.1693
30 H3 44.6515 39.3570 36.8437 H 1 LIG210 0.3481
31 HO3' 36.5607 38.9743 36.9843 H 1 LIG210 0.4373
32 HP3 39.3989 32.7036 35.9199 H 1 LIG210 0.4245
33 HO2' 39.5501 41.7087 35.4449 H 1 LIG210 0.4228
We need to manually rename the atoms.
22 H1 40.0697 36.0506 37.6716 H 1 LIG210 0.0761
23 H2 40.6060 37.0416 36.2883 H 1 LIG210 0.0349
24 H3 38.2510 37.5673 38.1082 H 1 LIG210 0.0967
25 H4 38.2723 38.5564 35.5613 H 1 LIG210 0.1052
26 H5 40.3056 39.7322 35.6920 H 1 LIG210 0.1188
27 H6 39.7587 40.5927 38.4795 H 1 LIG210 0.0753
28 H7 41.3847 41.7815 39.3543 H 1 LIG210 0.0322
29 H8 43.6843 42.3632 39.6188 H 1 LIG210 0.1693
30 H9 44.6515 39.3570 36.8437 H 1 LIG210 0.3481
31 HO1 36.5607 38.9743 36.9843 H 1 LIG210 0.4373
32 HP3 39.3989 32.7036 35.9199 H 1 LIG210 0.4245
33 HO2 39.5501 41.7087 35.4449 H 1 LIG210 0.4228
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, parmchk and tleap) and we are using the correct version of amber, we can use the which command, type:
which antechamber which parmchk which tleap
Your results should be similar to this:
/home/wjallen/AMS536/local/amber12/bin/antechamber /home/wjallen/AMS536/local/amber12/bin/parmchk /home/wjallen/AMS536/local/amber12/bin/tleap
Copy parameters of ions to your working directory from the following resource:
cp -r ~lingling/AMS536/AMBER_Tutorial/002.ANTE.TLEAP/rizzo_amber7.ionparms
Then we use antechamber to convert our input mol2 file into files ready for LEaP.Type command:
antechamber -i ../001.CHIMERA.MOL.PREP/1LOQ.lig.mol2 -fi mol2 -o 1LOQ.lig.ante.pdb -fo pdb
Here, -i input file name; -fi input file format; -o output file name; -fo output file format. You will have an output file:1LOQ.lig.ante.pdb
Similarly, we can use antechamber to change the fomat of 1LOQ.lig.mol2 file to prep file:
antechamber -i ../001.CHIMERA.MOL.PREP/1LOQ.lig.mol2 -fi mol2 -o 1LOQ.lig.ante.prep -fo prepi
You will get a set of output files:
ANTECHAMBER_AC.AC ANTECHAMBER_AC.AC0 ANTECHAMBER_BOND_TYPE.AC ANTECHAMBER_BOND_TYPE.AC0 ANTECHAMBER_PREP.AC ANTECHAMBER_PREP.AC0 ATOMTYPE.INF NEWPDB.PDB PREP.INF 1LOQ.lig.ante.prep
parmchk
Parmchk is another program in Antechamber. 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 1LOQ.lig.ante.prep -f prepi -o 1LOQ.lig.ante.frcmod
tleaP
Next, we need 3 new input files – “tleap.lig.in”, “tleap.rec.in” and “tleap.com.in”, for the ligand, the receptor, and the complex, respectively. These input files will be used by LEaP to create parameter/topology files and initial coordinate files.
Copy parameters of ions to your working directory from the following resource:
cp ~lingling/AMS536/AMBER_Tutorial/002.ANTE.TLEAP/tleap.lig.in cp ~lingling/AMS536/AMBER_Tutorial/002.ANTE.TLEAP/tleap.rec.in cp ~lingling/AMS536/AMBER_Tutorial/002.ANTE.TLEAP/tleap.com.in
Use leap command:
tleap -s -f tleap.lig.in > tleap.lig.out tleap -s -f tleap.rec.in > tleap.rec.out tleap -s -f tleap.com.in > tleap.com.out
You will see the following output files: 1LOQ.com.gas.leap.prm7 1LOQ.com.wat.leap.prm7 1LOQ.lig.ante.frcmod 1LOQ.lig.ante.prep 1LOQ.lig.gas.leap.rst7 1LOQ.lig.wat.leap.rst7 1LOQ.rec.gas.leap.rst7 1LOQ.rec.wat.leap.rst7 1LOQ.com.gas.leap.rst7 1LOQ.com.wat.leap.rst7 1LOQ.lig.ante.pdb 1LOQ.lig.gas.leap.prm7 1LOQ.lig.wat.leap.prm7 1LOQ.rec.gas.leap.prm7 1LOQ.rec.wat.leap.prm7 tleap.lig.out tleap.rec.out tleap.com.out leap.log
Visualization in VMD
Visualization is an important step in AMBER molecular dynamics simulation as it allows for the viewing of molecules and molecule movements within a specified field of view. Several files prepared in the previous two steps will be required for the visualization of the ligand and its movement in the protein binding pocket. The first step that must be completed is the copying of all necessary information from Seawulf to Herbie.
Before exiting Seawulf, you can type:
scp -r ~/AMS536/AMBER_Tutorial/002.ANTE.TLEAP username@herbie.mathlab.sunysb.edu:~/AMS536/AMBER_Tutorial/
Then, when in Herbie, type the command vmd in any directory and the program VMD will open on the computer. In the "VMD Main" window, click File > New Molecule. Now in the new window titled "Molecule File Browser" a few files must be selected and loaded. To select and load a file follow these steps: 1. Click Browse... and select the file that you desire. 2. Click the down button in the "Determine file type:" field and select the proper file type. 3. Click Load and view the molecule/system in the original "VMD 1.8.5 OpenGL Display" window.
III. Simulation using sander
Minimization
Equilibration
Production
Running jobs on the queue
To run equilibration and production, Write the tcsh file equil.produc.qsub.csh:
#! /bin/tcsh
#PBS -l nodes=4:ppn=2
#PBS -l walltime=720:00:00
#PBS -o zzz.qsub.out
#PBS -e zzz.qsub.err
#PBS -V
set workdir = "~lingling/AMS536/AMBER_Tutorial/003.SANDER"
cd ${workdir}
cat $PBS_NODEFILE | sort | uniq
mpirun -n 8 /nfs/user03/wjallen/local/amber12/bin/sander.MPI -O -i 01mi.in -o 01mi.out -p ../002.ANTE.TLEAP/1LOQ.com.wat.leap.prm7 \
-c ../002.ANTE.TLEAP/1LOQ.com.wat.leap.rst7 -ref ../002.ANTE.TLEAP/1LOQ.com.wat.leap.rst7 \
-x 01mi.trj -inf 01mi.info -r 01mi.rst7
mpirun -n 8 /nfs/user03/wjallen/local/amber12/bin/sander.MPI -O -i 02md.in -o 02md.out -p ../002.ANTE.TLEAP/1LOQ.com.wat.leap.prm7 \
-c 01mi.rst7 -ref 01mi.rst7 -x 02md.trj -inf 02md.info -r 02md.rst7
mpirun -n 8 /nfs/user03/wjallen/local/amber12/bin/sander.MPI -O -i 03mi.in -o 03mi.out -p ../002.ANTE.TLEAP/1LOQ.com.wat.leap.prm7 \
-c 02md.rst7 -ref 02md.rst7 -x 03mi.trj -inf 03mi.info -r 03mi.rst7
mpirun -n 8 /nfs/user03/wjallen/local/amber12/bin/sander.MPI -O -i 04mi.in -o 04mi.out -p ../002.ANTE.TLEAP/1LOQ.com.wat.leap.prm7 \
-c 03mi.rst7 -ref 03mi.rst7 -x 04mi.trj -inf 04mi.info -r 04mi.rst7
mpirun -n 8 /nfs/user03/wjallen/local/amber12/bin/sander.MPI -O -i 05mi.in -o 05mi.out -p ../002.ANTE.TLEAP/1LOQ.com.wat.leap.prm7 \
-c 04mi.rst7 -ref 04mi.rst7 -x 05mi.trj -inf 05mi.info -r 05mi.rst7
mpirun -n 8 /nfs/user03/wjallen/local/amber12/bin/sander.MPI -O -i 06md.in -o 06md.out -p ../002.ANTE.TLEAP/1LOQ.com.wat.leap.prm7 \
-c 05mi.rst7 -ref 05mi.rst7 -x 06md.trj -inf 06md.info -r 06md.rst7
mpirun -n 8 /nfs/user03/wjallen/local/amber12/bin/sander.MPI -O -i 07md.in -o 07md.out -p ../002.ANTE.TLEAP/1LOQ.com.wat.leap.prm7 \
-c 06md.rst7 -ref 06md.rst7 -x 07md.trj -inf 07md.info -r 07md.rst7
mpirun -n 8 /nfs/user03/wjallen/local/amber12/bin/sander.MPI -O -i 08md.in -o 08md.out -p ../002.ANTE.TLEAP/1LOQ.com.wat.leap.prm7 \
-c 07md.rst7 -ref 07md.rst7 -x 08md.trj -inf 08md.info -r 08md.rst7
mpirun -n 8 /nfs/user03/wjallen/local/amber12/bin/sander.MPI -O -i 09md.in -o 09md.out -p ../002.ANTE.TLEAP/1LOQ.com.wat.leap.prm7 \
-c 08md.rst7 -ref 08md.rst7 -x 09md.trj -inf 09md.info -r 09md.rst7
mpirun -n 8 /nfs/user03/wjallen/local/amber12/bin/sander.MPI -O -i 10md.in -o 10md.out -p ../002.ANTE.TLEAP/1LOQ.com.wat.leap.prm7 \
-c 09md.rst7 -ref 09md.rst7 -x 10md.trj -inf 10md.info -r 10md.rst7
mpirun -n 8 /nfs/user03/wjallen/local/amber12/bin/sander.MPI -O -i 11md.in -o 11md.out -p ../002.ANTE.TLEAP/1LOQ.com.wat.leap.prm7 \
-c 10md.rst7 -ref 09md.rst7 -x 11md.trj -inf 11md.info -r 11md.rst7
exit
Note in the above script that for each run, the .rst7, .trj and .info files generated from the previous run provides the initial state to start from. The .prm7 file generated for the hydrated complex by TLEAP provides the force parameters.
Submit the file to the queue and monitor progress.
IV. Simulation Analysis
Ptraj
RMSD Plots
Measuring h-bond distances
MM-GBSA Energy Calculation
MM/GBSA is the acronym for Molecular Mechanics/Generalized Born Surface Area. This part of AMBER combines molecular mechanics (MM) with both the electrostatic (PB) and nonpolar (SA) contribution to solvation . Topology files are needed for the receptor, ligand, and receptor-ligand complex. The trajectory files generate the coordinates. Therefore, molecular dynamics is used to generate a set of snapshots taken at fixed intervals from the trajectories. These snapshots are processed to remove solvent and generate the free energy of binding.
In the AMBER_Tutorial directory, create a new directory:
mkdir 005.MMGBSA
In this new directory, create the file gb.rescore.in containing:
Single point GB energy calc &cntrl ntf = 1, ntb = 0, ntc = 2, idecomp= 0, igb = 5, saltcon= 0.00, gbsa = 2, surften= 1.0, offset = 0.09, extdiel= 78.5, cut = 99999.0, nsnb = 99999, imin = 5, maxcyc = 1, ncyc = 0,
/
Then create a csh script, run.sander.rescore.csh, that contains the following lines of command:
#! /bin/csh #PBS -l nodes=1:ppn=2 #PBS -l walltime=24:00:00 #PBS -o zzz.qsub.out #PBS -e zzz.qsub.err #PBS -V
set workdir = "/nfs/user03/yechen1/AMBER-Tutorial/005.MMGBSA" set sander = "/nfs/user03/wjallen/local/amber12/bin/sander"
cd ${workdir}
$sander -O -i gb.rescore.in -o gb.rescore.out.com -p ../002.ANTE.TLEAP /1LOQ.com.gas.leap.prm7 \
-c ../002.ANTE.TLEAP/1LOQ.com.gas.leap.rst7 -y ../004.PTRAJ/1LOQ.com.trj.stripfit \
-r restrt.com -ref ../002.ANTE.TLEAP/1LOQ.com.gas.leap.rst7 -x mdcrd.com -inf mdinfo.com
$sander -O -i gb.rescore.in -o gb.rescore.out.lig -p ../002.ANTE.TLEAP/1LOQ.lig.gas.leap.prm7 \ -c ../002.ANTE.TLEAP/1LOQ.lig.gas.leap.rst7 -y ../004.PTRAJ/1LOQ.lig.trj.stripfit \ -r restrt.lig -ref ../002.ANTE.TLEAP/1LOQ.lig.gas.leap.rst7 -x mdcrd.lig -inf mdinfo.lig
$sander -O -i gb.rescore.in -o gb.rescore.out.rec -p ../002.ANTE.TLEAP/1LOQ.rec.gas.leap.prm7 \ -c ../002.ANTE.TLEAP/1LOQ.rec.gas.leap.rst7 -y ../004.PTRAJ/1LOQ.rec.trj.stripfit \ -r restrt.rec -ref ../002.ANTE.TLEAP/1LOQ.rec.gas.leap.rst7 -x mdcrd.rec -inf mdinfo.rec
exit
~ ~ ~ ~ ~ ~ ~ ~ Then this script should be sent to the queue, i.e., qsub the script using the commands:
qsub run.sander.rescore.csh
You can monitor your progress by typing
qstat -u username
When the job is complete, you will obtain the following output files: gb.rescore.out.com, gb.rescore.out.lig, and gb.rescore.out.rec In these files, the single point energy calculation results will be written for each individual frame. It will be found in the results section and the output file will have an infrastrucutre that is similar to the following:
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 3.6269E+03 1.8737E+01 1.0472E+02 CB 585
BOND = 580.2786 ANGLE = 1563.7704 DIHED = 2161.5659 VDWAALS = -1684.2762 EEL = -13809.8494 EGB = -2953.6681 1-4 VDW = 756.7767 1-4 EEL = 7260.2823 RESTRAINT = 0.0000 ESURF = 9752.0291 minimization completed, ENE= 0.36269092E+04 RMS= 0.187371E+02 TRAJENE: Trajectory file ended TRAJENE: Trajene complete.
In the command line, type:
grep VDWAALS gb.rescore.out.com > vdw.com.txt.
grep ESURF gb.rescore.out.com > surf.com.txt.
You can take these text files, import them into Excel, and do the rest of your modifications there.
Equations for analysis
Remember that to obtain the Gvdw term, you need to take the SASA (which is ESURF) and input into equation 1:
ΔGnonpolar = SASA*0.00542 + 0.92
Also, the mmgbsa of a given system can be determined by equation 2:
ΔGmmgbsa = ΔGvdw + ΔGcoul + ΔGpolar + ΔGnonpolar
From the output file:
VDWAALS = ΔGvdw
EELS = ΔGcoul
EGB = ΔGpolar
You can then easily calculate the ΔΔGbind by using equation 3:
ΔΔGbind = ΔGmmgbsa,complex – (ΔGmmgbsa,lig + ΔGmmgbsa,rec) You will want to careful when doing your analysis that the results from frame 1 for the receptor and ligand are subtracted from the results from frame 1 for your complex. By doing this in excel, you should have 2000 frames for each, and the values should cleanly line up. Finally, you will want to plot your ΔΔGbind and examine if you see corresponding changes in the ligand position and the ΔΔGbind. Also, you should determine the mean and standard deviation for your ΔΔGbind.
