Molecular Simulations Workshop:Molecular Simulations Workshop:Introductions/Amber: How to setIntroductions/Amber: How to set--up up

calculations (1)calculations (1)

-1-

Yeng-Tseng Wang

Email: c00jsw00@gmail.com

Applied Scientific Computing Division, National Center for High-Performance Computing

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Use of Molecular Dynamics SimulationKinetics and irreversible processes

•chemical reaction kinetics (with QM)

•conformational changes, allosteric mechanisms

•Protein folding

Equilibrium ensemble sampling

•Flexibility

•thermodynamics (free energy changes, binding)

Modeling tool

•structure prediction / modeling

•solvent effects

•NMR/crystallography (refinement)

•Electron microscopy (flexible fitting)

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Why use molecular dynamics?

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Why use molecular dynamics?

nm μm mm

fsec

psec

nsec

msec

TimeScale

SpaceScale

MolecularDynamicsQMD

Continuous Mechanics

Statistical Mechanics

Quantum Chemistry

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Atomic Detail Computer Simulation

Molecular Mechanics Potential

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⎢⎢

⎣

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⎞⎜⎜⎝

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θ PMF Surface →Exploration by Umbrella Sampling Simulations

© Yeng-Tseng Wang

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Bonded Interactions: StretchingEstr represents the energy required to stretch or compress a covalent bond:

A bond can be thought of as a spring having its own equilibrium length, ro, and the energy required to stretch or compress it can be approximated by the Hookean potential for an ideal spring:

Estr = ½ ks,ij ( rij - ro )2

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Bonded Interactions: BendingEbend is the energy required to bend a bond from its equilibrium angle, θo:

Again this system can be modeled by a spring, and the energy is given by the Hookean potential with respect to angle:

Ebend = ½ kb,ijk (θijk - θo )2

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Bonded Interactions: TorsionEtor is the energy of torsion needed to rotate about bonds:

© Thomas W. Shattuck

A

BC

D

E

F

φ

300200100000

1

2

3

Dihedral Angle

Dih

edra

l Ene

rgy

(kca

l/mol

)

CH3

HH

CH3

H

H

Butane

Torsional interactions are modeled by the potential:

Etor = ½ ktor,1 (1 - cos φ ) + ½ ktor,2 (1 - cos 2 φ ) + ½ ktor,3 ( 1 - cos 3 φ )

asymmetry (butane) 2-fold groups e.g. COO- standard tetrahedral torsions

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Non-Bonded Interactions: van derWaals

EvdW is the steric exclusion and long-range attraction energy (QM origins):

© Thomas W. Shattuck 65432-0.2

-0.1

0.0

0.1

0.2V an der Waals Int eract ion f or H.. . ..H

H. .. . H d ist ance ( Å )

Ene

rgy

( kc

al/m

ol

)

at t ract ion

repulsion

Two frequently used formulas:

E E

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Non-Bonded Interactions: CoulombEqq is the Coulomb potential function for electrostatic interactions of charges:

© Thomas W. Shattuck

Formula:

The Qi and Qj are the partial atomic charges for atoms i and j separated by adistance rij. ε is the relative dielectric constant. For gas phase calculations ε is normally set to 1. Larger values of ε are used to approximate the dielectric effect of intervening solute (ε∼60-80) or solvent atoms in solution. k is a units conversion constant; for kcal/mol, k=2086.4.

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Newton’s Law

Newton’s Law: iii amF =

Esteric energy = Estr + Ebend + Etor + EvdW + Eqq

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Verlet’s Numeric Integration Method

2)(!2

1)()()( ttrttrtrttr δδδ &&& ++=+

tttrtrtvttv δδδ ))()((21)()( +++=+ &&&&

r

v

F

t-δt t t+δt

r

v

F

t-δt t t+δt

r

v

F

t-δt t t+δt

r

v

F

t-δt t t+δt

r

v

F

t-δt t t+δt

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F

t-δt t t+δt

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F

t-δt t t+δt

r

v

F

t-δt t t+δt

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Timescale Limitations

•Protein Folding -milliseconds/seconds (10-3-1s)•Ligand Binding -micro/milliseconds (10-6-10-3 s)•Enzyme catalysis -micro/milliseconds (10-6-10-3 s)•Conformational transitions -pico/nanoseconds (10-12-10-9 s)•Collective vibrations -1 picosecond (10-12 s)•Bond vibrations -1 femtosecond (10-15 s)

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Timescale Limitations

Molecular dynamics:Integration timestep - 1 fs, set by fastest varying force.

Accessible timescale: about 10 nanoseconds.

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Cutting Corners

SHAKE

MTS

PME

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How to use Amber on NCHC ALPS cluster

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1. Putty ssh login: (ip: 140.110.140.6)ID：t00jsw00～t00jsw20 (2011/10/04～2011/10/07)2. vi command3. bash shell 4. cd /work ; mkdir t00jsw?? ; cd t00jsw?? 5. cp ../work/t00jsw00/amber11.workshop.tar .6. tar xvf amber.workshop.tar

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Amber: How to set-up calculations

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Preliminary RemarksPreliminary RemarksAmber is a very sophisticated piece of scientific software and as such requires some amount of time to learn it.

Although Amber may appear very complex at first, it is reasonably straightforward once you understand the basic architecture and option choices.

The best source of help for active users of the Amber software is the amber mailing list and the mailing list archive (http://ambermd.org/). Questions sent to this list will go to all active amber uses and so you get the help of the amber community.

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Preliminary RemarksPreliminary RemarksHave a look at the Amber Home Page: http://ambermd.org/

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Basic Steps for Running Simulation1. Obtain starting Coordinates (PDB,

NMR, Database, Program generated)2. Assigning force field 3. Run LEaP to generate the parameter and

topology file.4. Run Simulation (sander or pmemd)5. Analyse the results (ptraj)

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Information Flow in AmberInformation Flow in Amber

PDBantechamber

LEap

Topology andcoordinate files

sander, pmemd,pmemd.cuda

nmode

Simulation Results

ptrajmm-pbsa…

Analysis Programs

SimulationPrograms

Preparatory Programs

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Introduction to Introduction to LEaPLEaPThe name LEaP is an acronym constructed from the names of the older AMBER software modules it replaces: link, edit, and parm.Thus, LEaP can be used to prepare input for the AMBER molecular mechanics programs.LEaP is the generic name given to the programs teLeapand xaLeap, which are generally run via the tleap and xleap shell scripts.These two programs share a common command languageThe xleap program has been enhanced through the addition of an X-windows graphical user interface.

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Using Using tleaptleap, the user can:, the user can:Read and write files in many formats (PDB, Mol2, Amber Prep, Amber Parm, Object File Format) Construct new residues and molecules using simple commandsLink together residues and create nonbondedcomplexes of moleculesPlace counterions around a moleculeSolvate molecules in arbitrary solventsModify internal coordinates within a moleculeGenerate files that contain topology and parameters for AMBER.

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With With XleapXleap the user can:the user can:Access commands using a simple point and click interfaceDraw new residues and molecules in a graphical environmentView structures graphicallyGraphically dock moleculesModify the properties of atoms, residues, and molecules using a spreadsheet editorInput or alter molecular mechanics parameters using a spreadsheet editor.

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““StandardStandard”” Amber Amber Amino Acid ResiduesAmino Acid Residues

• The N-terminal amino acid names and aliases are prefaced by the letter N (e.g. NALA for N-terminal ALA) and the C-terminal amino acids by the letter C (e.g.CALA)

• Histidine can exist either as the protonatedspecies or as a neutral species with a hydrogen at the delta or epsilon position. For this reason, the histidine name is either HIP, HID, or HIE (but not HIS). By default LEaP assigns the name HIS to HIE.

• The AMBER force fields also differentiate between the residue cysteine (CYS) and the similar residue that participates in disulfide bridges, cystine (CYX).

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Specifying a force fieldSpecifying a force fieldls amber11/dat/leap/cmd

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Specifying force field in Specifying force field in LEaPLEaPxleap/tleap -s -f <filename>

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Introduction to Introduction to AntechamberAntechamberThis is a set of tools to generate files for organic molecules, which can then be read into LEaP.

It can perform many file conversions, and can also assign atomic charges and atom types

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Introduction to SanderIntroduction to SanderThe acronym stands for Simulated Annealing with NMR-Derived Energy Restraints

Sander is the Amber module which carries out energy minimization, molecular dynamics, and NMR refinements.

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Sander Sander Input DescriptionInput Descriptionsander [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt[-ref refc] [-x mdcrd] [-v mdvel] [-e mden] [-inf mdinfo]Arguments in []'s are optional

If an argument is not specified, the default name will be used. -O overwrite all output files (the default behavior is to quit if any output files already exist) -i the name of the input file (which describes the simulation options), mdin by default. -o the name of the output file, mdout by default. -p the parameter/topology file, prmtop by default. -c the set of initial coordinates for this run, inpcrd by default. -r the final set of coordinates from this MD or minimization run, restrt by default. -ref reference coordinates for positional restraints, if this option is specified in the input file, refc by default. -x the molecular dynamics trajectory file (if running MD), mdcrd by default. -v the molecular dynamics velocities file (if running MD), mdvel by default. -e a summary file of the energies (if running MD), mden by default. -inf a summary file written every time energy information is printed in the output file for the current step of the minimization of MD, useful for checking on the progress of a simulation, mdinfo by default.

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Preparation of Preparation of control data for the control data for the minimization/MD runminimization/MD run

Each of the variables listed below is input in a namelist statement with the namelist identifier &cntrl.

End of namelist &cntrl

Keyword identifier

Variables that are not given in the namelist input retain their default values.

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Preparation of Preparation of control data for Sandercontrol data for Sander

http://sf.anu.edu.au/~vvv900/cct/appl/sander8input/index.html1.Download program here (shift-click or right-mouse-click for download) 2.To run it issue the command "java -jar Sander8Input.jar" in command prompt or

double click on it (MS Windows, Mac OS)

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Tutorial 1 DNA simulationsTutorial 1 DNA simulations

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Tutorial 1 DNA simulations:Tutorial 1 DNA simulations:building DNA structuresbuilding DNA structures1. export AMBERHOME=XXXXX/amber112. export PATH=$PATH:$AMBERHOME/exe 3. nab nuc.nab4. ./a.out (nuc.pdb)

molecule m;

m = fd_helix( "abdna", "aaaaaaaaaa", "dna" );putpdb( "nuc.pdb", m, "-wwpdb");

nuc.nab:

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Tutorial 1 DNA simulations:Tutorial 1 DNA simulations:building DNA structuresbuilding DNA structures5. xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB 6. dna1=loadpdb "nuc.pdb" 7. edit dna1

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Tutorial 1 DNA simulations:Tutorial 1 DNA simulations:building DNA structuresbuilding DNA structures

8. list

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Tutorial 1 DNA simulations:Tutorial 1 DNA simulations:building DNA structuresbuilding DNA structures

9. charge dna1 (Therefore we need to add ions into the system.)

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Tutorial 1 DNA simulations:Tutorial 1 DNA simulations:building DNA structuresbuilding DNA structures

For implicit solvent model:10. saveamberparm dna1 polyAT_vac.prmtop polyAT_vac.inpcrd

For explicit solvent model:11. addions dna1 Na+ 012. dna2 = copy dna1 13. solvatebox dna1 TIP3PBOX 8.0

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Tutorial 1 DNA simulations:Tutorial 1 DNA simulations:building DNA structuresbuilding DNA structures

14. solvateoct dna2 TIP3PBOX 8.015. saveamberparm dna2 polyAT_wat.prmtop polyAT_wat.inpcrd savea

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Tutorial 1 DNA simulationsTutorial 1 DNA simulationsImplicit solvent simulations (Amber11.pdf : page~53 or Reference to MD.GB.pdf)Minimization16. $AMBERHOME/exe/sander -O -i polyAT_gb_init_min.in \-o polyAT_gb_init_min.out -c polyAT_vac.inpcrd \-p polyAT_vac.prmtop -r polyAT_gb_init_min.rst

polyA-polyT 10-mer: initial minimization prior to MD GB model&cntrlimin = 1, (To turn on minimization, we specify imin = 1 )maxcyc = 500, (500 steps of minimization )

ncyc = 250, (1st: steepest descent algorithm, 2nd: conjugate gradient method )ntb = 0, (periodic [PBC]: turn off )igb = 1, (generalized born solvation model )cut = 12 (non-bonded force evaluation: cutoff )/

polyAT_gb_init_min.in:

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Tutorial 1 DNA simulationsTutorial 1 DNA simulationsMD(12A cutoff)17. sander -O -i polyAT_gb_md1_12Acut.in -o polyAT_gb_md1_12Acut.out -c polyAT_gb_init_min.rst-p polyAT_vac.prmtop -r polyAT_gb_md1_12Acut.rst -x polyAT_gb_md1_12Acut.mdcrd

10-mer DNA MD Generalized Born, 12 angstrom cut off&cntrlimin = 0, ntb = 0, (minimization & PBC: turn off)igb = 1, ntpr = 100, ntwx = 100, (writing information and trajectories / 100 steps )ntt = 3, gamma_ln = 1.0, (temperature control :Langevin dynamics )tempi = 300.0, temp0 = 300.0 (initial and final temperatures: 300 K )nstlim = 100000, dt = 0.001,cut = 12.0/

polyAT_gb_md1_12Acut.in :

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Tutorial 1 DNA simulationsTutorial 1 DNA simulationsMD(999 A cutoff)18. sander -O -i polyAT_gb_md1_nocut.in -o \polyAT_gb_md1_nocut.out -c polyAT_gb_init_min.rst \-p polyAT_vac.prmtop -r polyAT_gb_md1_nocut.rst \-x polyAT_gb_md1_nocut.mdcrd

10-mer DNA MD Generalized Born, 12 angstrom cut off&cntrlimin = 0, ntb = 0, (minimization & PBC: turn off)igb = 1, ntpr = 100, ntwx = 100, (writing information and trajectories / 100 steps )ntt = 3, gamma_ln = 1.0, (temperature control :Langevin dynamics )tempi = 300.0, temp0 = 300.0 (initial and final temperatures: 300 K )nstlim = 100000, dt = 0.001,cut = 999.0/

polyAT_gb_md1_nocut.in:

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Tutorial 1 DNA simulationsTutorial 1 DNA simulationsAnalyzing the results: (Energies profiles)19. ambpdb –p *.prmtop <*.rst > *.pdb20. perl process_mdout.perl ../polyAT_gb_md1_12Acut.out 21. perl process_mdout.perl ../polyAT_gb_md1_nocut.out 22. xmgrace ./polyAT_gb_md1_12Acut/summary.EPTOT \./polyAT_gb_md1_nocut/summary.EPTOT

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Tutorial 1 DNA simulationsTutorial 1 DNA simulationsAnalyzing the results: (RMSd vs. time) (ptraj: reference to AmberTools.pdf)23. ptraj polyAT_vac.prmtop < polyAT_gb_md1_12Acut.calc_rms 24. ptraj polyAT_vac.prmtop < polyAT_gb_md1_nocut.calc_rms 25. xmgrace polyAT_gb_md1_12Acut.rms polyAT_gb_md1_nocut.rms

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Tutorial 1 DNA simulationsTutorial 1 DNA simulationsExplicit solvent simulations:Periodic boundary simulations (PBC) : particle mesh Ewald (PME)

ntb = 0 no periodicity & PME is off= 1 constant volume (default)= 2 constant pressure

Reference Amber11.pdf p . 35

2D schematic PME in most Fourier-based methods (a) A system of charged particles. (b) The charges are interpolated on a 2D grid. (c) Using FFT, the potential and forces are calculated at grid points. (d) Interpolate forces back to particles and update coordinates.

21

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Tutorial 1 DNA simulationsTutorial 1 DNA simulationsExplicit solvent simulations Minimization (For water box)26. sander -O -i polyAT_wat_min1.in -o polyAT_wat_min1.out -p polyAT_wat.prmtop -c polyAT_wat.inpcrd -r polyAT_wat_min1.rst -ref polyAT_wat.inpcrd

polyA-polyT 10-mer: initial minimization solvent + ions&cntrlimin = 1, (minimization: turn on)maxcyc = 1000, (associated minimization) ncyc = 500, (associated minimization)ntb = 1, (PBC: turn on)ntr = 1, (constraints: turn on)cut = 10.0

/Hold the DNA fixed500.0 (force constant :500 kcal/mol-A**2)RES 1 20ENDEND

polyAT_wat_min1.in:

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Tutorial 1 DNA simulationsTutorial 1 DNA simulationsExplicit solvent simulations Minimization (For whole system)27. sander -O -i polyAT_wat_min2.in -o polyAT_wat_min2.out -p polyAT_wat.prmtop -c polyAT_wat_min1.rst -r polyAT_wat_min2.rst

polyA-polyT 10-mer: initial minimization whole system&cntrlimin = 1,maxcyc = 2500,ncyc = 1000,ntb = 1,ntr = 0, (constraints: turn off)cut = 10.0

/

polyAT_wat_min2.in

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Tutorial 1 DNA simulationsTutorial 1 DNA simulationsSHAKE algorithm

The SHAKE algorithm calculates the constraint force G12 = - G21 that conserves the bond length d12 between atoms 1 and 2 following the initial movement to positions 1’ and 2’ under the unconstrained forces F1 and F2.

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Tutorial 1 DNA simulationsTutorial 1 DNA simulationsExplicit solvent simulations Molecular simulations: (restraints on the solute)28. sander -O -i polyAT_wat_md1.in -o polyAT_wat_md1.out -p polyAT_wat.prmtop -c polyAT_wat_min2.rst -r polyAT_wat_md1.rst -x polyAT_wat_md1.mdcrd -ref polyAT_wat_min2.rst

polyA-polyT 10-mer: 20ps MD with res on DNA&cntrlimin = 0,irest = 0, ntx = 1, (generating random initial velocities from a Boltzmann distribution)ntb = 1, cut = 10.0,ntr = 1, (restraints : turn on)ntc = 2, ntf = 2, (SHAKE should be turned on and used to constrain bonds involving hydrogen)tempi = 0.0, temp0 = 300.0,ntt = 3, gamma_ln = 1.0, (temperature control :Langevin dynamics)nstlim = 10000, dt = 0.002ntpr = 100, ntwx = 100, ntwr = 1000 (ntwr: writing a restart file)/Keep DNA fixed with weak restraints10.0RES 1 20 (ds-DNA)ENDEND

polyAT_wat_md1.in

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Tutorial 1 DNA simulationsTutorial 1 DNA simulationsExplicit solvent simulations Molecular simulations: (on the whole system)29. sander -O -i polyAT_wat_md2.in -o polyAT_wat_md2.out -p polyAT_wat.prmtop -c polyAT_wat_md1.rst -r polyAT_wat_md2.rst -x polyAT_wat_md2.mdcrd

polyA-polyT 10-mer: 100ps MD&cntrlimin = 0, irest = 1, ntx = 7, (NTX = 7 which means the coordinates, velocities and box information will be read from restart file. )ntb = 2, pres0 = 1.0, ntp = 1 , taup = 2.0,

( constant pressure PBC with an average pressure of 1 atm (PRES0). Isotropic position scaling should be used to maintain the pressure (NTP=1) and a relaxation time of 2ps should be used (TAUP=2.0). )cut = 10.0, ntr = 0,ntc = 2, ntf = 2,tempi = 300.0, temp0 = 300.0,ntt = 3, gamma_ln = 1.0,nstlim = 50000, dt = 0.002,ntpr = 100, ntwx = 100, ntwr = 1000/

polyAT_wat_md2.in

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Tutorial 1 DNA simulationsTutorial 1 DNA simulationsExplicit solvent simulations Analyzing30. Perl process_mdout.perl ../polyAT_wat_md1.out ../polyAT_wat_md2.out

31. ptraj polyAT_wat.prmtop < polyAT_wat_calc_backbone_rms.in32. xmgrace polyAT_wat_backbone.rms

trajin polyAT_wat_md1.mdcrdtrajin polyAT_wat_md2.mdcrdrms first out polyAT_wat_backbone.rms @P,O3',O5',C3',C4',C5' time 0.2

polyAT_wat_calc_backbone_rms.in

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Tutorial 1 DNA simulationsTutorial 1 DNA simulationsSimulations on Amber CUDA code (PMEMD.CUDA)http://ambermd.org/gpus/#Running

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Tutorial 1 DNA simulationsTutorial 1 DNA simulationsSimulations on Amber CUDA code (PMEMD.CUDA)http://ambermd.org/gpus/#Running

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Tutorial 1 DNA simulationsTutorial 1 DNA simulationsSimulations on Amber CUDA code (PMEMD.CUDA)

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Tutorial 1 DNA simulationsTutorial 1 DNA simulationsSimulations on Amber CUDA code (PMEMD.CUDA)

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Tutorial 1 DNA simulationsTutorial 1 DNA simulations

Simulations Times

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