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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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slide1

M.Orozco

J.L.Gelpí

M.Rueda

J.R.Blas

No a la

Guerra

slide4

NMR, X-Ray,...

QM, crystal data, experiments,...

nucgen

Estructura

Parámetros

( Construcción de ác. nucléicos )

resp

Antechamber

( Ajuste de cargas electrostáticas )

( Set-up automatizado )

LEaP

coordinate_file

topology_file

nmode

Obtención de

datos útiles en NMR

( Análisis de modos normales )

LES

sander

gibbs

intense

profec

( Estrategia especial de aumento de sampling conformaciona en MD )

( Dinámica molecular)

( Cálculo de diferencias de energía libre )

spectrum

( Genera grids de reactividad basadas en energía libre )

fantasian

Programas

de análisis

ptraj

carnal

anal

MM-PBSA

( Análisis de energías )

( Cálculo de energías libres )

( Procesado de trayectorias )

slide5

NMR, X-Ray,...

QM, crystal data, experiments,...

Estructura

Parámetros

LEaP

coordinate_file

topology_file

SANDER

( Dinámica molecular)

Programas

de análisis

ptraj

carnal

anal

MM-PBSA

( 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
  • IBELLY:
    • 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
shake
SHAKE
  • 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
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
PARTICLE MESH EWALD
  • &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
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
NMR REFINEMENT
  • ISCALE: Number of additional variables to optimize (in addition to 3N coordinates)
  • NOESKP: How often are the NOESY volumes computed
  • IPNLTY:
    • 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)
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