Molecular Dynamics Simulation

A computer simulation based on Newtons laws of motions and developed to study the motion of molecules over a period of time. 1. Molecular dynamics simulation is actually an in-silico simulation of the atomistic motions of a molecule. 2. These motions are governed by the Newtons Laws of Motion. 3. To apply the Laws, one needs the initial position (starting coordinates, available in pdb files), the acceleration calculated from force (F=ma). 4. The co-ordinates are calculated for each time-step upto the provided time period (say 10ns). 5. The force is calculated from the formula, = , where V is the potential energy. 6. The potential energy is calculated from the atomic interactions based on the following formula (taking into account bond stretching, angle bending, dihedral movements, electrostatic interactions and Van der Waals interactions).

The Force-Field

Topology Files (*.rtf)

!RTF File for Acetate MASS 1 HGA3 1.00800 MASS 2 CG2O3 12.01100 MASS 3 CG331 12.01100 ! aliphatic C for methyl group (-CH3) MASS 4 OG2D2 15.99940 ! carbonyl O: negative groups: carboxylates, carbonate RESI ACET -1.00 ! C2H3O2 acetate, K. Kuczera GROUP ATOM C1 CG331 -0.37 ! ATOM C2 CG2O3 0.62 ! H1 O1 (-) ATOM H1 HGA3 0.09 ! | / ATOM H2 HGA3 0.09 ! H2--C1--C2 ATOM H3 HGA3 0.09 ! | \\ ATOM O1 OG2D2 -0.76 ! H3 O2 ATOM O2 OG2D2 -0.76 ! BOND C1 H1 C1 H2 C1 H3 BOND C1 C2 C2 O1 DOUBLE C2 O2 IMPR C2 O2 O1 C1 IC O1 C2 C1 H1 0.00 0.00 0.0 0.00 0.00 IC C2 H1 *C1 H2 0.00 0.00 120.0 0.00 0.00 IC C2 H1 *C1 H3 0.00 0.00 -120.0 0.00 0.00 IC C1 O1 *C2 O2 0.00 0.00 180.0 0.00 0.00 PATC FIRS NONE LAST NONE

!RTF File RESI GLYN GROUP ATOM N ATOM HT1 ATOM HT2 ATOM CA ATOM HA1 ATOM HA2 GROUP ATOM C ATOM OT1 ATOM OT2 ATOM HO2

for Neutral Glycine 0.00 ! C2H5NO2 neutral glycine ! NG321 -0.96 ! HGPAM2 0.34 ! HT1 HT2 HGPAM2 0.34 ! \ / CG321 0.18 ! N HGA2 0.05 ! | HGA2 0.05 ! HA1-CA-HA2 ! | CG2O2 0.75 ! C OG2D1 -0.55 ! // \ OG311 -0.63 ! OT1 OT2 HGP1 0.43 ! | ! HO2 ! BOND N CA CA C C OT2 OT2 HO2 BOND N HT1 N HT2 CA HA1 CA HA2 DOUBLE OT1 C DONO HT1 N DONO HT2 N DONO HO2 OT2 IMPR C CA OT1 OT2

IC N CA C OT1 IC N CA C OT2 IC OT1 OT2 *C CA IC CA C OT2 HO2 IC C CA N HT1 IC C CA N HT2 IC N C *CA HA1 IC N C *CA HA2 PATCHING FIRS NONE LAST

1.5010 1.5010 1.2218 1.5780 1.5780 1.5780 1.5010 1.5010 NONE

119.00 119.00 117.44 113.44 119.00 119.00 119.00 119.00

88.76 -111.57 -161.57 -168.97 164.86 -77.98 120.0 -120.0

126.10 113.44 113.44 107.16 110.99 111.22 110.0 110.0

1.2218 1.3958 1.5780 0.9565 1.0023 1.0030 1.1 1.1

!RTF File for Acetic Acid RESI ACEH 0.00 ! C2H4O2 acetic acid, ADM jr. GROUP ATOM C2 CG331 -0.30 ! ATOM C1 CG2O2 0.75 ! H21 O2 ATOM H21 HGA3 0.09 ! \ // ATOM H22 HGA3 0.09 ! H22-C2--C1 ATOM H23 HGA3 0.09 ! / \ ATOM O2 OG2D1 -0.55 ! H23 O1-HO1 ATOM O1 OG311 -0.60 ! ATOM HO1 HGP1 0.43 ! BOND C1 O1 O1 HO1 C1 C2 C2 H21 C2 H22 C2 H23 DOUBLE C1 O2 IMPR C1 C2 O2 O1 DONO BLNK HO1 ! O1 ACCE O1 ACCE O2 IC O2 C1 C2 H21 0.0000 0.0000 0.0000 0.0000 IC HO1 O1 C1 O2 0.0000 0.0000 0.0000 0.0000 IC HO1 O1 C1 C2 0.0000 0.0000 180.0000 0.0000 IC O1 C1 C2 H21 0.0000 0.0000 180.0000 0.0000 IC O1 C1 C2 H22 0.0000 0.0000 60.0000 0.0000 IC O1 C1 C2 H23 0.0000 0.0000 -60.0000 0.0000

0.0000 0.0000 0.0000 0.0000 0.0000 0.0000

In the first part of the topology files the atom types to be used in the file are declared along with their atomic weight. RESI specifies the residue name to be written. Group specifies the atom groups remaining together (usually a single group for a small molecule) and the partial charges (theoretical). BOND specifies the bonding information i. e. the atom connectivity. DOUBLE specifies the double bonds. IMPR specifies the improper dihedrals. DONO and ACCE specifies the donor-acceptor partners. IC specifies the internal coordinates (not the integrated circuits!!!!) with the angles mentioned in the middle column.

Parameter Files (*.prm/ *.par)

! Parameter file MASS 1 HGA3 MASS 2 CG2O3 MASS 3 CG331 MASS 4 OG2D2 carbonate
BONDS CG1N1 CG1N1 CG1N1 CG1T1 CG1T1

for Acetate 1.00800 12.01100 12.01100 ! aliphatic C for methyl group (-CH3) 15.99940 ! carbonyl O: negative groups: carboxylates,

CG2R61 CG331 NG1T1 CG1T1 CG331

345.00 400.00 1053.00 960.00 410.00

1.4350 ! 3CYP, 3-Cyanopyridine (PYRIDINE pyr-CN) (MP2 by kevo) 1.4700 ! ACN, acetonitrile, kevo 1.1800 ! ACN, acetonitrile; 3CYP, 3-Cyanopyridine (PYRIDINE pyr-CN) (MP2 by kevo) 1.2200 ! 2BTY, 2-butyne, kevo 1.4650 ! 2BTY, 2-butyne, kevo

ANGLES CG2R61 CG1N1

NG1T1

40.00 21.20 19.00 40.00 40.00

CG331 CG1N1 NG1T1 CG1T1 CG1T1 CG331 CG25C1 CG251O CG2R53 CG25C1 CG251O NG2R53

CG25C1 CG251O SG311 CG2DC3 CG251O CG2R53 CG2DC3 CG251O NG2R53 DIHEDRALS HGA3 CG1T1

40.00 40.00 40.00

180.00 ! 3CYP, 3-Cyanopyridine (PYRIDINE pyrCN), yin 180.00 ! ACN, acetonitrile, kevo 180.00 ! 2BTY, 2-butyne, kevo 125.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy 124.00 ! OIHY, 5-(oxindol-3ylidene)hydantoin, complete ring system, xxwy 124.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy 119.00 ! MRDN, methylidene rhodanine, kevo & xxwy 130.00 ! MHYO, 5-methylenehydantoin, xxwy

CG1T1

HGA3

0.0005 6.4000 6.4000 3.4000

3 2 2 2

CG2R53 CG251O CG25C1 CG2R53 CG2R53 CG251O CG25C1 CG2RC0 NG2R53 CG251O CG25C1 CG2R53

NG2R53 CG251O CG25C1 CG2RC0

3.4000

SG311

CG251O CG25C1 CG2R53

6.4000

180.00 !!Just a test! 2BTY, 2butyne, kevo 180.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy 180.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy 180.00 ! OIHY, 5-(oxindol-3ylidene)hydantoin, complete ring system, xxwy 180.00 ! OIHY, 5-(oxindol-3ylidene)hydantoin, complete ring system, xxwy 180.00 ! OIRD, oxindol-3-ylidene rhodanine, kevo & xxwy

IMPROPERS CG2D1 CG331 CG2D1 CG331 CG2D1O CG2D1 CG2D1O CG2D1 CG2D1O CG2D2 CG2D1O CG2D2

NG2D1 NG2P1 NG301 NG311 NG321 OG301

HGA4 HGR52 HGA4 HGA4 HGA4 HGA4 HGA4

25.0000 18.0000 53.0000 53.0000 53.0000 23.0000 53.0000

0 0 0 0 0 0 0

CG2D1O CG2DC1 NG301

0.00 ! SCH1, xxwy 0.00 ! SCH2, xxwy 0.00 ! NA NICH, adm jr. WILDCARD 0.00 ! NA NICH, adm jr. WILDCARD 0.00 ! AMET, ethenamine, from NA NICH WILDCARD; pram 0.00 ! MOET, Methoxyethene, xxwy 0.00 ! NA NICH, adm jr. WILDCARD

NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !see mass list above for better description of atom types !hydrogens HGA1 0.0 -0.0450 1.3400 ! alkane, igor, 6/05 HGA2 0.0 -0.0350 1.3400 ! alkane, igor, 6/05 HGA3 0.0 -0.0240 1.3400 ! alkane, yin and mackerell, 4/98 HGA4 0.0 -0.0310 1.2500 ! alkene, yin,adm jr., 12/95 HGA5 0.0 -0.0260 1.2600 ! alkene, yin,adm jr., 12/95 HGA6 0.0 -0.0280 1.3200 ! fluoro_alkanes HGA7 0.0 -0.0300 1.3000 ! fluoro_alkanes HGAAM0 0.0 -0.0280 1.2800 ! aliphatic amines HGAAM1 0.0 -0.0280 1.2800 ! aliphatic amines HGAAM2 0.0 -0.0400 1.2600 ! aliphatic amines HGP1 0.0 -0.0460 0.2245 ! polar H HGP2 0.0 -0.0460 0.2245 ! small polar Hydrogen, charged systems HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use ! READ PARAM APPEND CARD ! to append hbond parameters from the file: par_hbond.inp

END

Running an MDS
Basic Steps:1. 2. 3. 4. 5. 6. 7. Reading the references (topology and parameter files), Reading a sequence from a sequence file/a pdb file Solvation in a waterbox and ion placements. Periodic boundary condition setup. Pressure/temperature condition setup. Equilibration run to stabilize the system temperature. Production run.

Without going into much details, CHARMM-GUI, a web server maintained by Wonpil Im Group at the University of Kansas, provides comprehensive support to ease the pain of these steps In CHARMM-GUI, you just have to upload/provide the pdb id or file and then you can ultimately set it up for a production run. CHARMM-GUI will provide you with all the files you need to run the simulation.

Setting Up A System Using A Web-Server

1. Go to http://www.charmm-gui.org. 2. Go to Input Generator available in the left pane. 3. Click on Quick MD Simulator in the same pane. 4. Provide the PDB ID or upload a file and mention its format (CHARMM/RCSB). 5. Click on Next Step: Select Model/Chain. 6. Select the protein chains and/or the crystallization water molecules. 7. Click on Next Step: Manipulate PDB. 8. Apply options available on the PDB. You can apply patch, phosphorylation or mention disulfide bonds, protonate residues etc. 9. Click on Next Step: Generate PDB. 10. Mention waterbox size and ion concentration. (Default ion concentration is 0.15 M KCl). The computed energy values for the protein are available now. 11. Click on Next Step: Solvate Molecule. 12. Crystal size details are shown in this page. Click on Next Step: Setup Periodic Boundary Conditions. 13. Click on Next Step: NVT Equilibration. If you notice, youll find the processed files in the boxed area and you can download them in your computer to process them manually. 14. Select the ensemble type. (NPT/NVT) and click on Next Step: Generate Dynamics Input. 15. Input files are ready for kicking start a molecular dynamics simulation. You can download the whole set of processed/unprocessed/intermediate files with all the scripts and topology/parameter files in a zipped format using the download .tgz button.

A Sample Dynamics Input File

* GENERATED BY CHARMM-GUI (http://www.charmm-gui.org) VERSION on Nov, 19. 2013. * INPUT FILE FOR NPT DYNAMICS OF SOLVATED GLOBULAR PROTEIN * ! Read topology and parameter files stream toppar.str ! Read PSF and Coordinates open read unit 10 card name step3_pbcsetup.psf read psf unit 10 card open read unit 10 card name step4_equilibration.crd read coor unit 10 card ! ! Setup PBC (Periodic Boundary Condition) ! stream step3_pbcsetup.str open read unit 10 card name crystal_image.str CRYSTAL DEFINE @XTLtype @A @B @C @alpha @beta @gamma CRYSTAL READ UNIT 10 CARD !Image centering by residue IMAGE BYRESID XCEN @xcen YCEN @ycen ZCEN @zcen sele resname TIP3 end IMAGE BYRESID XCEN @xcen YCEN @ycen ZCEN @zcen sele ( segid @posid .or. segid @negid ) end ! ! Nonbonded Options ! nbonds atom vatom vfswitch bycb ctonnb 10.0 ctofnb 12.0 cutnb 16.0 cutim 16.0 inbfrq -1 imgfrq -1 wmin 1.0 cdie eps 1.0 ewald pmew fftx @fftx ffty @ffty fftz @fftz kappa .34 spline order 6 energy ! !use a restraint to place center of mass of the molecules near the origin ! MMFP GEO rcm sphere Xref @xcen Yref @ycen Zref @zcen XDIR 1.0 YDIR 1.0 ZDIR 1.0 harmonic FORCE 1.0 select .not. ( hydrogen .or. resname TIP3 .or. segid @posid .or. segid @negid ) end END !

! ! ! ! ! !

NPT dynamics : you can change nstep : number of MD steps nprint : print-out frequency nsavc : the trajectory saving frequency

! estimate Pmass from SYSmass (total system mass) ! [there could be problems with exreme values, such as Pmass >> SYSmass scalar mass stat calc Pmass = int ( ?stot / 50.0 ) shake bonh param fast open read unit 11 card name step5.1_production.rst open write unit 12 card name step5.2_production.rst open write unit 13 file name step5.2_production.dcd

Pmass << SYSmass or

DYNA CPT leap restart time 0.002 nstep 10000 nprint 100 iprfrq 1000 ntrfrq 1000 iunread 11 iunwri 12 iuncrd 13 iunvel -1 kunit -1 nsavc 500 nsavv 0 PCONSTANT pref 1.0 pmass @Pmass pgamma 20.0 HOOVER reft 300.0 tmass 2000.0 tbath 300.0 firstt 300.0 open write unit 10 card name step5.2_production.pdb write coor unit 10 pdb open write unit 10 card name step5.2_production.crd write coor unit 10 card close unit 10 stop

The marked area points out the script needed to run a molecular dynamics simulation. In this case, it runs a dynamics of 10000 steps with 2 femtosecond time step. 2 femtosecond time step actually allows us to quantify and visualize even the bond vibrations. The temperature remains constant throughout the dynamics at 300K (i. e. 27oC aka room temperature). The dynamics uses the leapfrog-verlet integrator to solve the motion equations at every step. Being a restart dynamics, it reads the previous dynamics data from the file opened in unit number 11 and also saves a restart file for further use in unit number 12. The trajectory file (i. e. the file containing the co-ordinates of the molecules at every time step) is saved in unit number 13 in a .dcd format. The final pdb file is saved as step5.2_production.pdb and the co-ordinate file is saved as step5.2_production.crd.

Visualizing in VMD
Visual Molecular Dynamics or VMD 1.9.1 software is available for free from the University of Illinois-Urbana Champaigns Theoretical Biophysics Group webpage at http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD VMD is used to visualize, analyze and save pdb, trajectories etc. RMSD calculations, alignment and a lot of other calculations can be performed on the dynamics outputs along with representing them in several representations.

1. VMD Main : File -> New Molecule -> Browse pdb (1.pdb) -> load 2. File -> New Molecule -> Browse dcd (1.dcd) -> load 3. Play 4. Graphics -> Representation -> Drawing Method -> New Cartoon 5. Create representation , Selected Atoms: resname N3C (ligand), Drawing Method -> Licorice 6. Create representation , Selected Atoms: Protein and noh, Drawing Method -> Licorice 7. Extensions -> Analysis -> RMSD Trajectory Tool 8. Selection Modifiers: Backbone, check the plot option -> click on RMSD

9. To save the data : File -> Save data 10. Create representation , Drawing Method -> HBonds 11. Extension -> Analysis -> Hydrogen Bonds, click on Find hydrogen bonds! 12. To save the data : File -> Export to ASCII matrix 13. Surface representation : Create representation, Selected Atoms: Protein , Drawing Method -> Surface 14. Distance Scan : (i) Press 2 in the keyboard (ii) Select two atoms a) any C atom of the SPh group b) one F atom (iii) Graphics -> Labels -> Bonds -> Graphs

Material prepared by:1. Atanu Maity (Email:- atanuchem48@gmail.com) 2. Souparno Adhikary (Email:- souparnoadhikary@gmail.com)