Workshop on Molecular Dynamics

March 18, 2011

Tutorial

Complied by,
Girinath G. Pillai
Research & Teaching Associate, CBi
www.giribio.weebly.com

Vellore Institute of Technology

Vellore

Courtesy: http://www.ks.uiuc.edu
 Girinath G Pillai , CBi NAMD Tutorial 2

Molecular Dynamics using NAMD

Download VEGA ZZ release 2.0.8 or greater http://www.vegazz.net/

NAMD installation

 Download the Win32-i686 package from the Theoretical and Computational Biophysics Group web site.

 Unzip the package in the VEGA ZZ installation directory (usually C:\Program Files\VEGA ZZ).

 Rename the NAMD_X.X_Win32-i686 directory in NAMD (X.X is the NAMD version).

Protein download

You can download the protein (eg:insulin) structure using the PDB Web interface or the tool integrated in VEGA ZZ:

 Open the protein molecule in the work space.

 Normalize the coordinates in order to translate the protein at the origin of the Cartesian axis (Edit -> Coordinates -
> Normalize).

 Save the molecule (File -> Save As) with the insulin file name. It's strongly recommended the use of the IFF/RIFF file
format because it's able to keep the maximum number of information (e.g. atom types, charges, bond orders, etc).

Protein preparation:

1. Add Hydrogen to the molecule using the option Edit-> Add -> Hydrogens, selecting Protein in the Molecule type
box to enable an extra check for the atom hybridization, Residue end in the Position of hydrogens box and
checking Use IUPAC atom nomenclature. Finally, click Add to place the hydrogens.

2. Fix atom types and charges (Calculate – charge and Plot). Check Force field and Charges and selecting
CHARMM22_PROT and CHARMM22_CHAR. Click the Fix button.

3. Save the molecule in iff format. (Over writing the previous one)

Creation of Input files for NAMD

1. Save the molecule in Pdb 2.2 format

2. Create topological matrix in Xplor PSF format. (Also --- edit------ Auto assign and save as in the .inp file from the
displayed table)

3. Copy in the directory where are placed the insulin.pdb and insulin.psf files, the par_all22_prot.inp and
par_all22_vega.inp parameter files that are in the ...\VEGA ZZ\Data\Parameters directory. The
par_all22_vega.inp is required because VEGA ZZ generates a topology making explicit all improper angles.
3 NAMD Tutorial Girinath G Pillai, CBi

Create a command file (insulin_min.namd name)

With a text editor (e.g. Notepad) create the input file with the following commands

numsteps 10000
minimization on
dielectric 1.0
coordinates insulin.pdb
outputname insulin
outputEnergies 1000
binaryoutput no
DCDFreq 1000
restartFreq 1000
structure insulin.psf
paraTypeCharmm on
parameters par_all22_prot.inp
parameters par_all22_vega.inp
exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 8.0
cutoff 12.0
pairlistdist 13.5
margin 0.0
stepspercycle 20

Run NAMD file:

Open the VEGA console (Start -> VEGA ZZ -> VEGA console).

Go to inside your working directory with the cd command.

In the console type:

namd2 insulin_min.namd

If the program dint runs successfully try adding [Parameters insulin.inp ]inp file created during “autoassign” in the
command file

Analysis of results:

1. Open the dcd file. Trajectory analysis dialog will be opened. [Calculate-- Analysis]

2 .Click the Last or lowest button to get the lowest energy conformation.

3. Save the best conformation in .iff format (insulin _min.iff)

Minimization Using the atom constraints

In order to keep the structure more close to the original crystallographic data, a common procedure is to apply atom
constraints to the protein backbone. In this way, the side chains can relax themselves keeping the secondary structure.
NAMD and VEGA ZZ allow to constraint the atoms in two modes: fixing the atoms or applying a force constant to the
atoms restraining their movements.
 Girinath G Pillai , CBi NAMD Tutorial 4

i) Atom Fixing

1. Open the insulin.iff file

2. Open the Constraints options window (Edit -> Coordinates -> Constraints).

3. Select Fix in the Mode box and Protein backbone in the Selection box. Finally, click the Apply button and close the
window. The fixed atoms (the backbone) will be colored in blue and the free atoms in green.

4. Save the molecule in PDB 2.2 format, checking Constraints in the Options box and typing insulin _fix.pdb as file
name.

 Repeat the energy minimization with the following command file: insulin _fix_min.namd

numsteps 10000
minimization on
dielectric 1.0
coordinates insulin _fix.pdb
outputname insulin _fix
outputEnergies 1000
binaryoutput no
DCDFreq 1000
restartFreq 1000
structure insulin.psf
paraTypeCharmm on
parameters par_all22_prot.inp
parameters par_all22_vega.inp
exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 8.0
cutoff 12.0
pairlistdist 13.5
margin 0.0
stepspercycle 20
fixedAtoms on
fixedAtomsCol B

Start the minimization, typing in the console:

namd2 insulin _fix_min.namd > insulin _fix.out

Open the trajectory file. You can't open the trajectory file directly, if it doesn't exist the correspondent molecule file (e.g.
insulin _fix.iff). As first step, you must open the molecule and thus select Calculate -> Analysis in the menu bar. In the
Trajectory analysis window, click the open button and select the DCD file. Select and save the lowest energy conformation
as insulin _fix_min.iff.

ii) Atom constraints:

1. Open the insulin.iff file

2. Select Value in the Mode box, put 20 in the Value field of the Parameters box and choose Protein backbone in the
Selection box.
3. Save the file in PDB 2.2 format, checking the constraints in option box (insulin_const.pdb)
5 NAMD Tutorial Girinath G Pillai, CBi

Repeat the energy minimization with the following command file:[ insulin _const_min.namd]

numsteps 10000
minimization on
dielectric 1.0
coordinates insulin _const.pdb
outputname insulin _const
outputEnergies 1000
binaryoutput no
DCDFreq 1000
restartFreq 1000
structure insulin.psf
paraTypeCharmm on
parameters par_all22_prot.inp
parameters par_all22_vega.inp
exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 8.0
cutoff 12.0
pairlistdist 13.5
margin 0.0
stepspercycle 20
constraints on
consref insulin _const.pdb
conskfile insulin _const.pdb
conskcol B

 Start the minimization, typing in the console:

namd2 insulin _const_min.namd > insulin _const.out
 At the end of the minimization, open the trajectory file, select and save the lowest energy conformation as insulin
_const_min.iff.

In a water cluster:
1. To insert the molecule in a spherical/box water cluster, choose the Edit -> Add -> Cluster menu item and the
Cluster calculation window is opened.
2. Choose the solvent type (WATER), the cluster type (Sphere/Box in the Type box), set the sphere radius to 12.0
Å and click the Ok button.
3. Color the molecule by atom (View -> Color -> By atom).
4. Fix the atom types and the charges (Calculate -> Charge & Pot.), checking Force field and Charges and
selecting CHARMM22_PROT and Gasteiger. The total charge is -1.
5. Save the molecule in IFF format, naming the file insulin _wat.iff (File -> Save As...).
6. Save the molecule in PDB 2.2 format (insulin _wat.pdb). This file is required by NAMD and it doesn't need the
PDB connectivity and so you can avoid to save it unchecking Connectivity in the Options box.
PSF file creation
 Save the molecule in X-Plor PSF format (insulin _wat.psf), selecting the force field name in the Force field param.
box. The CHARMM22_PROT force field was used in the atom type attribution and so you must select the same
force field. This operation is useful to check if all parameters needed by the insulin are included in the force field
parameter file.

The Missing parameter table will be shown:

It indicates all angles, bonds and torsions parameters not included in the force field. In this window you can put manually
the parameters, but if you don't know them, you can ask to the program to complete them for you.
Click Edit -> Auto assign and the table will be filled. Please remember that this isn't a full exaustive approach and it can
generate wrong parameters. To check them, you can click on the missing parameter in the table and the involved atoms
are automatically highlighted in the workspace.
Filled the table, save the parameter file selecting File -> Save As... in the menu bar of the Missing parameter table
window. Use insulin _wat.inp as file name.

numsteps 5000
minimization on
dielectric 1.0
coordinates insulin _wat.pdb
outputname insulin _wat_min
 Girinath G Pillai , CBi NAMD Tutorial 6

outputEnergies 1000
binaryoutput no
DCDFreq 1000
restartFreq 1000
structure insulin _wat.psf
paraTypeCharmm on
parameters par_all22_prot.inp
parameters par_all22_vega.inp
parameters insulin _wat.inp
exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 8.0
cutoff 12.0
pairlistdist 13.5
margin 0.0
stepspercycle 20

Save the file with the insulin_wat_min.namd name. This performs a 5000 steps conjugate gradients minimization, saving the
output (coordinates and restart files) every 1000 iterations.

 Open the VEGA console (Start -> VEGA ZZ -> VEGA console).
 Go to inside your working directory with the cd command.
 In the console, type:
namd2 insulin_wat_min.namd
and hit return. After few time the minimization is finish.
 Select Calcualte -> Analysis and open the insulin _wat_min.dcd trajectory file, clicking the open button.
 Click the Lowest button and save the lowest energy frame selecting File -> Save As... in the main window. Choose
the PDB 2.2 format and insulin _wat_min.pdb as file name.

Heating
This is the first molecular dynamics phase required to set the atom velocities at the specified temperature.
 In a text editor (e.g. Notepad), copy & paste the following commands:

numsteps 3000
dielectric 1.0
coordinates insulin _wat_min.pdb
temperature 0
seed 12345
outputname insulin _wat_heat
outputEnergies 1000
binaryoutput yes
DCDFreq 1000
restartFreq 1000
timestep 1.0
nonbondedFreq 1
fullElectFrequency 1
structure insulin _wat.psf
paraTypeCharmm on
parameters par_all22_prot.inp
parameters par_all22_vega.inp
parameters insulin _wat.inp
exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 8.0
cutoff 12.0
pairlistdist 13.5
margin 0.0
stepspercycle 20
langevin on
langevinDamping 10
langevinTemp 300
langevinHydrogen no
7 NAMD Tutorial Girinath G Pillai, CBi

sphericalBC on
sphericalBCCenter 0.0 0.0 0.0
sphericalBCr1 16.00
sphericalBCk1 2.00

Save the file with insulin _wat_heat.namd name. This input file performs a 0 to 300 K heating, using the Langevin algorythm
and setting the spherical harmonic boundary conditions defining a virtual sphere of 16 Å radius, centered at the axis origin
(0, 0, 0), using 2 as exponent of the boundary potential. These last parameters are required to reduce the solvent
evaporation. For more information about the NAMD configuration, see the on-line documentation.
Start the heating, typing in the console:
namd2 insulin _wat_heat.namd > insulin _wat_heat.out
and hit return.

Molecular dynamics
At the heating end, you must prepare the MD input file.
 In a text editor, copy & paste the following commands:
firsttimestep 3000
numsteps 103000
dielectric 1.0
coordinates insulin _wat_min.pdb
bincoordinates insulin _wat_heat.coor
binvelocities insulin _wat_heat.vel
extendedsystem insulin _wat_heat.xsc
seed 12345
outputname insulin_wat_dyn
outputEnergies 1000
binaryoutput yes
DCDFreq 1000
restartFreq 1000
timestep 1.0
nonbondedFreq 1
fullElectFrequency 1
structure insulin_wat.psf
paraTypeCharmm on
parameters par_all22_prot.inp
parameters par_all22_vega.inp
parameters insulin _wat.inp
exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 8.0
cutoff 12.0
pairlistdist 13.5
margin 0.0
stepspercycle 20
langevin on
langevinDamping 10
langevinTemp 300
langevinHydrogen no
sphericalBC on
sphericalBCCenter 0.0 0.0 0.0
sphericalBCr1 16.00
sphericalBCk1 2.00
 Save the file with insulin _wat_dyn.namd name. This input file performs a 100 ps molecular dynamics at 300 K
constant temperature.
 To run the molecular dynamics, type:
namd2 insulin_wat_dyn.namd > insulin_wat_dyn.out
and hit return.

You can contact me at http://giribio.weebly.com

 Girinath G Pillai , CBi NAMD Tutorial 8

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