TRAPP-structure workflow

Currently the following methods can be used to compute possible protein conformational changes:

  • tCONCOORD
  • L-RIP and RIPlig (Langevin-rotamerically induced perturbation and rotamerically induced perturbation of the ligand)
  • MD (implicit solvent with SASA; Langevin dynamics; NAMD)

MD

Parameters used:

  • force field: charmm27
  • exclude scaled 1-4
  • 1-4scaling 1.0

# cutoffs:

  • switching on
  • switchDist 14.0
  • cutoff 17.0
  • pairListDist 18.0

# minimization parameters:

  • minimization on
  • numsteps 800
  • outputenergies 200

#GBIS parameters:

  • GBIS on
  • ionConcentration 0.3
  • alphaCutoff 15
  • SASA on
  • GBISDelta 1.0
  • GBISBeta 0.8
  • GBISGamma 4.85

Additionally for heating:

# temperature coupling:

  • langevin on
  • langevinHydrogen on
  • set temperature 300
  • langevinDamping 5.0



# constant pressure heating:

  • for {set i 10} {$i < $temperature} {incr i 25}
  • set tempr $i
  • langevinTemp $tempr
  • reinitvels $tempr
  • run 100
  • firsttimestep 0 ;
  • # reset frame counter:
  • reinitvels $temperature

Additionally for equilibration:

  • numSteps 1000
  • timeStep 2 # fs
  • rigidBonds all
  • firstTimeStep 0
  • stepsPerCycle 10

Additionally for MD:

  • timeStep 2 # fs
  • rigidBonds all
  • firstTimeStep 0
  • stepsPerCycle 12
  • nonBondedFreq 2
  • fullElectFrequency 4

# temperature coupling:

  • langevin on
  • langevinHydrogen on
  • langevinTemp 300
  • langevinDamping 5.0