# Minimization and Equilibration of phosphorylated MDM2 in water box # The basic protocol for MD simulations consists of minimization (to eliminate initial contacts # which would destabilize the integrator), equilibration to a temperature of 300 K and a pressure # of 1 atm, and simulation in an isobaric (NPT) ensemble for 1-10 ns. cwd /home/ambrish/HIV2/mode2/equilibration # working directory for simulation seed 1234567 #Molecular System structure Mode2_wb_neutral.psf # PSF file name coordinates Mode2_wb_neutral.pdb # Input coordinate file set temperature 310; temperature $temperature ; firsttimestep 0 #Force field Parameters paraTypeCharmm on # use CHARMM-type PSF <=> default is XPLOR. parameters par_all27_prot_na.prm # CHARMM parameter file parameters toppar_prot_na_all.str # CHARMM topology file for phosphorylated Serine # Output parameters binaryoutput off outputEnergies 100 # Default is 1 i.e. every step outputTiming 100 # Default is 0, i.e. never outputPressure 100 DCDfreq 1000 restartfreq 1000 xstFreq 1000 cellBasisVector1 73.08 00.00 00.00 cellBasisVector2 00.00 58.66 00.00 cellBasisVector3 00.00 00.00 73.01 cellOrigin -1.15337276459 5.0900349617 17.4325790405 wrapWater on wrapAll on wrapNearest on margin 5 Pme on PmeGridsizeX 80 PmeGridsizeY 60 PmeGridsizeZ 80 exclude scaled1-4 1-4scaling 1.0 switching on cutoff 12.0 # Where the electrostatic interaction is truncated. switchdist 10.0 pairlistdist 13.5 # Distance larger than cutoff where forces might not be felt stepspercycle 20 # Redo pairlist every ? steps # Integrator Parameters timestep 1.0 # This is in fs nonBondedFreq 2 fullElectFrequency 4 fixedAtoms on fixedAtomsForces on fixedAtomsFile fix_backbone.pdb fixedAtomsCol B constraints on consRef restrain_ca.pdb consKFile restrain_ca.pdb consKCol B langevin on langevinDamping 10 langevinTemp $temperature ; langevinHydrogen no langevinPiston on langevinPistonTarget 1.01325 langevinPistonPeriod 100. langevinPistonDecay 50. langevinPistonTemp $temperature ; useGroupPressure yes # smaller fluctuations useFlexibleCell no # allow dimensions to fluctuate independently useConstantRatio no # fix shape in x-y plane outputname mode2_equilibration # run one step to get into scripting mode minimize 0 # turn off until later langevinPiston off #Minimize Non-backbone atoms minimize 1000 output mode2_min_fix #Minimize all atoms fixedAtoms off minimize 1000 output mode2_min_all #Heat with CAs restrained run 3000 output mode2_heat # equilibrate volume,cell area,energy without restraints langevinPiston on run 20000 output mode2_equil_ca constraintScaling 0 run 100000