Molecular Simulations Workshop:

Introductions/Amber: How to set-up

calculations (1)
Applied Scientific Computing Division, National Center
for High-Performance Computing
Yeng-Tseng Wang
Email: c00jsw00@gmail.com

-1-

Use of Molecular Dynamics Simulation

Kinetics 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)
2

Why use molecular dynamics?

Why use molecular dynamics?

Time
Scale
msec
Continuous Mechanics

nsec
psec
fsec

Quantum
Chemistry

Molecular
QMD Dynamics

nm

Statistical
Mechanics

mm

Space
Scale
4

Atomic Detail Computer Simulation

Molecular Mechanics Potential

V=

k (b b )

bonds

k ( )

angles
N

K( )[1 + cos(n )] + K ( )

dihedrals n =1

impropers

12 6
qq
+ 4 ij ij ij + i j
r i , j Dr
rij
i, j
ij
ij

PMF Surface
Exploration by Umbrella
Sampling Simulations
Yeng-Tseng Wang

Bonded Interactions: Stretching

Estr 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 = ks,ij ( rij - ro )2
6

Bonded Interactions: Bending

Ebend is the energy required to bend a bond from its equilibrium angle, o:

Again this system can be modeled by a spring, and the energy is given by the
Hookean potential with respect to angle:
Ebend = kb,ijk (ijk - o )2
7

Bonded Interactions: Torsion

Etor is the energy of torsion needed to rotate about bonds:

CH3

Thomas W. Shattuck

Dihedral Energy (kcal/mol)

CH3

Butane

0
0

100
200
Dihedral Angle

300

Torsional interactions are modeled by the potential:

Etor = ktor,1 (1 - cos ) + ktor,2 (1 - cos 2 ) + ktor,3 ( 1 - cos 3 )
asymmetry (butane)

2-fold groups e.g. COO-

standard tetrahedral torsions

Non-Bonded Interactions: van der

Waals
EvdW is the steric exclusion and long-range attraction energy (QM origins):
V an de r Wa a ls Int e ra ct ion f or H .. . .. H

Ene rg y ( k c al / m o l )

0 .2

0 .1

r epul sio n

0 .0

-0 .1
at t ract io n

-0 .2

Thomas W. Shattuck

4
H. .. . H d ist a nc e ( )

Two frequently used formulas:

E
9

Non-Bonded Interactions: Coulomb

Eqq 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 a
distance rij. is the relative dielectric constant. For gas phase calculations is
normally set to 1. Larger values of are used to approximate the dielectric effect
of intervening solute (60-80) or solvent atoms in solution. k is a units conversion
constant; for kcal/mol, k=2086.4.

10

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

Newtons Law:

Fi = mi ai

11

Verlets Numeric Integration Method

1
r (t + t ) = r (t ) + r&(t )t + &r&(t )t 2
2!
1
v(t + t ) = v(t ) + (&r&(t ) + &r&(t + t ))t
2
t-t

t+t

t-t

t+t

t-t

t+t

t-t

t+t

12

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)
13

Timescale Limitations

Molecular dynamics:
Integration timestep - 1 fs, set by
fastest varying force.
Accessible timescale: about 10
nanoseconds.

14

Cutting Corners

PME

SHAKE
MTS

15

How to use Amber on NCHC ALPS

cluster

16

1. Putty ssh login: (ip: 140.110.140.6)

IDt00jsw00t00jsw20 (2011/10/042011/10/07)
2. vi command
3. bash shell
4. cd /work ; mkdir t00jsw?? ; cd t00jsw??
5. cp ../work/t00jsw00/amber11.workshop.tar .
6. tar xvf amber.workshop.tar

17

Amber: How to set-up calculations

18

Preliminary Remarks
Amber 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.

19

Preliminary Remarks
Have a look at the Amber Home Page: http://ambermd.org/

20

Basic Steps for Running Simulation

1.
2.
3.
4.
5.

Obtain starting Coordinates (PDB,

NMR, Database, Program generated)
Assigning force field
Run LEaP to generate the parameter and
topology file.
Run Simulation (sander or pmemd)
Analyse the results (ptraj)

21

Information Flow in Amber

PDB

antechamber
LEap

Preparatory Programs

Analysis Programs
Topology and
coordinate files

mm-pbsa
Simulation
Programs

ptraj

sander, pmemd,
pmemd.cuda
nmode
Simulation Results

22

Introduction to LEaP
The 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 teLeap
and xaLeap, which are generally run via the tleap and
xleap shell scripts.
These two programs share a common command
language
The xleap program has been enhanced through the
addition of an X-windows graphical user interface.

23

Using tleap, 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 commands
Link together residues and create nonbonded
complexes of molecules
Place counterions around a molecule
Solvate molecules in arbitrary solvents
Modify internal coordinates within a molecule
Generate files that contain topology and
parameters for AMBER.
24

With Xleap the user can:

Access commands using a simple point and click
interface
Draw new residues and molecules in a graphical
environment
View structures graphically
Graphically dock molecules
Modify the properties of atoms, residues, and
molecules using a spreadsheet editor
Input or alter molecular mechanics parameters
using a spreadsheet editor.

25

Standard Amber
Amino 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 Cterminal amino acids by the letter C
(e.g.CALA)
Histidine can exist either as the protonated
species 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).
26

Specifying a force field

ls amber11/dat/leap/cmd

27

Specifying force field in LEaP

xleap/tleap -s -f <filename>

28

Introduction to Antechamber
This 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

29

Introduction to Sander
The 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.

30

Sander Input Description

sander [-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.

31

Preparation of control data for the

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

Keyword identifier

End of namelist &cntrl

Variables that are not given in the namelist input retain their default values.
32

Preparation of control data for Sander

http://sf.anu.edu.au/~vvv900/cct/appl/sander8input/index.html

1.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)
33

Tutorial 1 DNA simulations

34

Tutorial 1 DNA simulations:

building DNA structures
1. export AMBERHOME=XXXXX/amber11
2. export PATH=$PATH:$AMBERHOME/exe
3. nab nuc.nab
4. ./a.out (nuc.pdb)
nuc.nab:
molecule m;
m = fd_helix( "abdna", "aaaaaaaaaa", "dna" );
putpdb( "nuc.pdb", m, "-wwpdb");

35

Tutorial 1 DNA simulations:

building DNA structures
5. xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
6. dna1=loadpdb "nuc.pdb"
7. edit dna1

36

Tutorial 1 DNA simulations:

building DNA structures
8. list

37

Tutorial 1 DNA simulations:

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

38

Tutorial 1 DNA simulations:

building DNA structures
For implicit solvent model:
10. saveamberparm dna1 polyAT_vac.prmtop polyAT_vac.inpcrd
For explicit solvent model:
11. addions dna1 Na+ 0
12. dna2 = copy dna1
13. solvatebox dna1 TIP3PBOX 8.0

39

Tutorial 1 DNA simulations:

building DNA structures
14. solvateoct dna2 TIP3PBOX 8.0
15. saveamberparm dna2 polyAT_wat.prmtop polyAT_wat.inpcrd savea

40

Tutorial 1 DNA simulations

Implicit solvent simulations (Amber11.pdf : page~53 or Reference
to MD.GB.pdf)
Minimization
16. $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
polyAT_gb_init_min.in:
polyA-polyT 10-mer: initial minimization prior to MD GB model
&cntrl
imin = 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 )
/
41

Tutorial 1 DNA simulations

MD(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
polyAT_gb_md1_12Acut.in :
10-mer DNA MD Generalized Born, 12 angstrom cut off
&cntrl
imin = 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
/
42

Tutorial 1 DNA simulations

MD(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
polyAT_gb_md1_nocut.in:
10-mer DNA MD Generalized Born, 12 angstrom cut off
&cntrl
imin = 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
/
43

Tutorial 1 DNA simulations

Analyzing the results: (Energies profiles)
19. ambpdb p *.prmtop <*.rst > *.pdb
20. 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

44

Tutorial 1 DNA simulations

Analyzing 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

45

Tutorial 1 DNA simulations

Explicit 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.

46

Tutorial 1 DNA simulations

Explicit 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
polyAT_wat_min1.in:
polyA-polyT 10-mer: initial minimization solvent + ions
&cntrl
imin = 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 fixed
500.0 (force constant :500 kcal/mol-A**2)
RES 1 20
END
END

47

Tutorial 1 DNA simulations

Explicit 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
polyAT_wat_min2.in
polyA-polyT 10-mer: initial minimization whole system
&cntrl
imin = 1,
maxcyc = 2500,
ncyc = 1000,
ntb = 1,
ntr = 0, (constraints: turn off)
cut = 10.0
/

48

Tutorial 1 DNA simulations

SHAKE 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.

49

Tutorial 1 DNA simulations

Explicit 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
polyAT_wat_md1.in
polyA-polyT 10-mer: 20ps MD with res on DNA
&cntrl
imin = 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 = 0.002
ntpr = 100, ntwx = 100, ntwr = 1000 (ntwr: writing a restart file)
/
Keep DNA fixed with weak restraints
10.0
RES 1 20 (ds-DNA)
END
END

50

Tutorial 1 DNA simulations

Explicit 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
polyAT_wat_md2.in
polyA-polyT 10-mer: 100ps MD
&cntrl
imin = 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
/

51

Tutorial 1 DNA simulations

Explicit solvent simulations
Analyzing
30. Perl process_mdout.perl ../polyAT_wat_md1.out ../polyAT_wat_md2.out
31. ptraj polyAT_wat.prmtop < polyAT_wat_calc_backbone_rms.in
32. xmgrace polyAT_wat_backbone.rms

polyAT_wat_calc_backbone_rms.in
trajin polyAT_wat_md1.mdcrd
trajin polyAT_wat_md2.mdcrd
rms first out polyAT_wat_backbone.rms @P,O3',O5',C3',C4',C5' time 0.2

52

Tutorial 1 DNA simulations

Simulations on Amber CUDA code (PMEMD.CUDA)
http://ambermd.org/gpus/#Running

53

Tutorial 1 DNA simulations

Simulations on Amber CUDA code (PMEMD.CUDA)
http://ambermd.org/gpus/#Running

54

Tutorial 1 DNA simulations

Simulations on Amber CUDA code (PMEMD.CUDA)

55

Tutorial 1 DNA simulations

Simulations on Amber CUDA code (PMEMD.CUDA)

56

Tutorial 1 DNA simulations

Simulations on Amber CUDA code (PMEMD.CUDA)

Costing Times

500

1.2

450
400

350
300
250

GB(pmemd)
Tip3(pmemd)

200
150
100
50

Costing Times (%)

Time (second)

Simulations Times

0.8
GB(pmemd)

0.6

Tip3(pmemd)

0.4
0.2

GTX 460

ALPS 48 core

GTX 460

ALPS 48 core

57