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M.Orozco J.L.Gelp M.Rueda J.R.Blas - PowerPoint PPT Presentation

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M.Orozco J.L.Gelpí M.Rueda J.R.Blas. No a la Guerra. Clase 6: Detalles de la simulación. SANDER. NMR, X-Ray,. QM, crystal data, experiments,. nucgen. Estructura. Parámetros. ( Construcción de ác. nucléicos ). resp. Antechamber. ( Ajuste de cargas electrostáticas ).

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No a la


NMR, X-Ray,...

QM, crystal data, experiments,...




( Construcción de ác. nucléicos )



( Ajuste de cargas electrostáticas )

( Set-up automatizado )





Obtención de

datos útiles en NMR

( Análisis de modos normales )






( Estrategia especial de aumento de sampling conformaciona en MD )

( Dinámica molecular)

( Cálculo de diferencias de energía libre )


( Genera grids de reactividad basadas en energía libre )



de análisis





( Análisis de energías )

( Cálculo de energías libres )

( Procesado de trayectorias )

NMR, X-Ray,...

QM, crystal data, experiments,...







( Dinámica molecular)


de análisis





( Análisis de energías )

( Cálculo de energías libres )

( Procesado de trayectorias )

Descripci n general simulaci n
Descripción general simulación

  • TIMLIM: Tiempo límite CPU simulación

  • IMIN: Decisión tipo cálculo

    • 0: Dinámica

    • 1: Minimización

  • NMROPT: Flag NMR

    • 0: No NMR restrains

    • >0: NMR restrains/weight changes

    • 2: NOESY volume restraints or chemical shifts restrains

Nature format of the input
Nature & Format of the input

  • NTX: Read coordinates, velocities and box

    • 1: X formatted no V

    • 5: X and V are read formatted

    • 7: X,V and Box are read formatted

  • IREST: Flag to restart the run:

    • 0 No

    • 1 Restart (need X, V)

  • NTRX: Format for restraint from file refc

    • 0 unformatted

    • 1 formatted

Nature format of the output
Nature & Format of the output

  • NTX0: Format for coordinates velocities and box

    • 1: X formatted

    • 0: unformatted

  • NTPR: Every NTPR mdifo will be printed.

  • NTWR: Every NTWR restart file will be written.

  • IWRAP: 1 Center solute in the primary box.

Nature format of the output1
Nature & Format of the output

  • NTWX, NTWV, NTWE: frequency of the output of coordinates, velocities, energies (If .ne. 0)

  • NTWXM, NTWVM, NTWEM: If .ne. 0 limits the output of coordinates, velocities, energies

  • NTWPRT: archive limit flag (V,X)

    • 0 all atoms

    • <0 only solute

    • >0 only atoms 1NTWPRT

Potential function
Potential function

  • NTF Force evaluation

    • 1: complete interaction

    • 2: bonds involving H are omitted

    • 3: all the bonds are omitted

    • ...

  • NTB Periodic boundary conditions

    • 0: No periodicity

    • 1: Constant volume

    • 2: Constant pressure

Potential function1
Potential function

  • DIELC: multiplicative factor for dielectric constant default 1.0. See options in GB/SA

  • CUT: Cutoff for non-bonded interactions. See Ewald

  • SCNB: Scaling of 1-4 vW interactions (1/SCNB). Default 2

  • SCEE: Scaling of 1-4 electrostatic (1/SCEE). Default 1.2

Potential function gb calculations
Potential functionGB calculations

  • IGB: Use of generalized Born model (GB) IGB=0 no GB, IGB=1., IGB=2 (vacuum calculation), IGB=3 (vacuum distance dependent dielc const.)

  • GBPARM: 1 (Beveridge), 2 (Case) Two sets of GB parameters

  • READRAD: if .ne.0 read vW radii for GB calculations

  • OFFSET: fine tune of Born radii defaults 0.09 or 0

  • IGBFREQ: Frequency of update of Born radii

  • GBSA: If .eq.1 SA corrections to GB.

  • SURFTEN: Use non-default surface tension.

Generalized born
Generalized Born

Método de introducir solvente continuo

Técnica potente pero poco contrastada

No recomendada para no expertos

Potential function polarizable potentials
Potential functionPolarizable potentials

  • IPOL. Inclusion of polarization

    • 0 No polarization

    • 1 Use polarization

    • 2 Use polarization + 3 body interactions

No recomendado para no expertos

Potential function frozen restrained atoms
Potential functionFrozen/restrained atoms


    • 0 normal run

    • 1 Belly run. Only a set of atoms (specified later) are allowed to move

  • NTR: Restraints in the Cartesian space (use harmonic restraints)

    • 0 No restraints

    • 1 MD with restraints on specific atoms

Energy minimization
Energy minimization

  • MAXCYC: Maximum number of cycles.

  • NCYC: After NCYC change from one method of optimization to other.

  • NTMIN: Method for minimization

    • 0 Conjugate gradient

    • 1 For NCYC steepest descent then CG

    • 2 Only steepest descent

  • DX0, DXM, DRMS: Details of minimization procedure: Use defaults

Molecular dynamics
Molecular dynamics

  • NSTLIM: Number of MD-steps per NRUN to be performed

  • NDFMIN: Number degrees of freedom to remove. If NTCM or NSCM.ne.0 use 6, otherwise 0.

  • NTCM:

    • 0 Do not remove translational/rotational moves around center of mass

    • 1 Remove at the beginning

  • NSCM: Remove translational/rotational moves around center of mass every NSCN steps (def 0)

  • T: Time at the start, default 0.0

  • DT: Integration time

Etapa de integraci n
Etapa de integración

  • Si no constraints en ningún enlace 0.0005 ps.

  • Si constraints (SHAKE) en enlaces X-H 0.001 ps

  • Si constraints en todos los enlaces 0.002

  • Si el sistema esta muy tensionado, T o P es elevada usar 0.001 ps

  • Reducir la etapa de integración aumenta linealmente el costo de la simulación pero puede ser necesario para evitar discontinuidades

Regulaci n de la temperatura
Regulación de la temperatura

  • TEMP0: Reference temperature

  • TEMPI: Starting temperature. Flag important when random velocities are generated.

  • IG: Seed random number for velocity calculation

  • NTT: Temperature scaling

    • 0 Constant energy run. No scaling

    • 1 Constant T. Use Berendsen’s coupling

    • 4 When T deviates from TEMP0 more than DTEMP scale velocities, otherwise do not scale

  • TAUTP: Time constant for heat bath coupling: Default 1.0. Smaller value tighter coupling

  • VLIMIT: IF .ne.0 when velocity of one atom is >VLIMIT set velocity=VLIMIT

Regulaci n de la presi n ntb 2
Regulación de la presión(NTB=2)

  • NTP: Flag for constant pressure dynamics

    • 0 no constant pressure

    • 1 MD isotropic scaling

    • 2 MD anisotropic scaling

  • PRES0: Pressure (1 atm default).

  • COMP: Compressibility of the system. In general use water value (44.6)

  • TAUP: Pressure relaxation time (0.2 ps)

  • NPSCAL: Modelo de escalado posiciones

    • 0: atom scaling: can compress bonds.

    • 1: Molecule scaling


  • NTC: Flag to use SHAKE (In general a good idea for normal systems)

    • 1 Do not use SHAKE

    • 2 SHAKE on X-H bonds

    • 3 SHAKE on all the bonds

  • TOL: Tolerance for coordinate resetting in SHAKE. Default 0.0005 Å.

Water cap gota de agua
WATER CAP(gota de agua)

  • IVCAP:

    • 0 in effect if defined in parm

    • 1 Cap in effect, but pointer will be modified (MATCAP)

    • 2 Cap will be inactivated

  • FCAP:

    • Force constant for Cap (half harmonic). Default 1.5 kcal/mol Å2

Particle mesh ewald

  • Es una técnica muy poderosa para incluir interacciones electrostática de largo alcance.

  • Es totalmente necesaria para simular DNA

  • Recomendable para proteínas, sobre todo si están muy cargadas

  • Sobreestima la periodicidad de la simulación.

  • Últimas versiones de AMBER lo toman como defecto de la simulación.

Particle mesh ewald1

  • &ewald namelist

    • A,B,C. The PME unit cell

    • Alpha,Beta,GAMMA: Cell angles

    • NFFT1,NFFT2,NFFT3: Size of charge grid. In general choose =A,B,C i.e grid spacing 1 Å

    • Use defaults for all the other parameters

Nmr refinement

  • La mayoría de usuarios usa MD solo para refinar la geometría a partir de las restricciones de distancias o ángulos derivadas a partir de otros programas DIANA,...

  • Estas restricciones se introducen como “flat harmonic restraints” que se añaden al force-field.

  • Es posible introducir otras restricciones más elaboradas: Time averaged restrains, noesy volumes, dipolar couplings,...

Nmr refinement1

  • ISCALE: Number of additional variables to optimize (in addition to 3N coordinates)

  • NOESKP: How often are the NOESY volumes computed


    • 1 minimize the abs value of errors (R-factor)

    • 2 minimize the RMS (sum square errors)

    • 3 Special treatment for NOESY intensities

  • MXSUB: Number of submolecules to be use def 1

Restraints file
Restraints file

  • IRESID (restraints definition)

    • 0 global atom numbers

    • 1 global residue number

  • IAT(1)IAT(4) if IRESID=0 atoms to restraints (IAT(3)=0, distance, IAT(4)=0 angle, otherwise torsion). If IRESID=1 residue number, then ATNAM(1)ATNAM(2) define the atom #s.

  • NSTEP1, NSTEP2 use restraints only between these two integration steps. Def uses always 0

  • IRSTYP: Absolute (0) or relative (1) restraints

Restraints file1
Restraints file

  • IALTD: Ignore large violation if 1. If 0 (default) not ignore

  • IFVARI: Change force or target value along the trajectory (R1AR4A, RK2ARK3A.

  • NINC, IMULT: Define how the target/force values change along the trajectory (use defaults).

Restraints file2
Restraints file

  • La forma del restraints es un pozo plano (si IALTD=0, default)

    • R1R4; RK2RK3; R1AR4A; RK2RK3

  • Si R (valor en la simulación)

    • R<r1 o R>4. Liniar slope restraint

    • R2<R<R3 E=0 (flat)

    • Parabolic constraint otherwise

  • La forma del restraints varia para IALTD=1

Restraints file3
Restraints file

  • IGR1(i),i=1200. IGR2(i), =1200. Se usan para definir restraints sobre un grupo de átomos. Se calculan promedio de posiciones con esas listas

Other restraints used for nmr refinement
Other restraints (used for NMR refinement)

  • Es posible incluir restraints adicionales

    • NOESY volume restraints

    • Chemical shifts restraints

    • Direct dipolar coupling restraints

    • Restraints de quiralidad

    • Time-averaged constraints

  • Se puede activar opción LES (multiple-copies)