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
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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.
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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 minimization dielectric coordinates outputname outputEnergies binaryoutput DCDFreq restartFreq structure paraTypeCharmm parameters parameters exclude 1-4scaling switching switchdist cutoff pairlistdist margin stepspercycle
10000 on 1.0 insulin.pdb insulin 1000 no 1000 1000 insulin.psf on par_all22_prot.inp par_all22_vega.inp scaled1-4 1.0 on 8.0 12.0 13.5 0.0 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 command file
insulin.inp ]inp file created during “autoassign” in the
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
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 minimization dielectric coordinates outputname outputEnergies binaryoutput DCDFreq restartFreq structure paraTypeCharmm parameters parameters exclude 1-4scaling switching switchdist cutoff pairlistdist margin stepspercycle fixedAtoms fixedAtomsCol
10000 on 1.0 insulin _fix.pdb insulin _fix 1000 no 1000 1000 insulin.psf on par_all22_prot.inp par_all22_vega.inp scaled1-4 1.0 on 8.0 12.0 13.5 0.0 20 on 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)
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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 minimization dielectric coordinates outputname
5000 on 1.0 insulin _wat.pdb insulin _wat_min
Girinath G Pillai , CBi
NAMD Tutorial
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 dielectric coordinates temperature seed outputname outputEnergies binaryoutput DCDFreq restartFreq timestep nonbondedFreq fullElectFrequency structure paraTypeCharmm parameters parameters parameters exclude 1-4scaling switching switchdist cutoff pairlistdist margin stepspercycle langevin langevinDamping langevinTemp langevinHydrogen
3000 1.0 insulin _wat_min.pdb 0 12345 insulin _wat_heat 1000 yes 1000 1000 1.0 1 1 insulin _wat.psf on par_all22_prot.inp par_all22_vega.inp insulin _wat.inp scaled1-4 1.0 on 8.0 12.0 13.5 0.0 20 on 10 300 no
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NAMD Tutorial sphericalBC sphericalBCCenter sphericalBCr1 sphericalBCk1
Girinath G Pillai, CBi on 0.0 0.0 0.0 16.00 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
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