############################################################# ## JOB DESCRIPTION ## ############################################################# # Minimization of B7-1 in a Cubic Water Box ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# # Amber/(t,s,x)leap generated parm and crd file cwd . parmfile ../common/solvated_g1I8LA.prmtop coordinates ../common/g1I8LA_leap.pdb ;# use either coordinates or ambercoor (.inpcrd file) set temperature 310 set outputname min firsttimestep 0 ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input amber on temperature $temperature # parameters # AMBER Force-Field Parameters exclude scaled1-4 readexclusions yes 1-4scaling 0.833333 # =1/1.2 (SCEE), default value is 1.0 for CHARMM force field scnb 2.0 ;# default value for both CHARMM and AMBER cutoff 9.0 switching off #pairlistdist 11.0 ;# specify pairlist when switching is on # Integrator Parameters timestep 2.0 ;# 2fs/step rigidBonds all ;# needed for 2fs steps rigidTolerance 0.0005 ;# Default is 0.00001 nonbondedFreq 1 fullElectFrequency 2 stepspercycle 10 # Constant Temperature Control langevin on ;# do langevin dynamics langevinDamping 1 ;# damping coefficient (gamma) of 1/ps langevinTemp $temperature langevinHydrogen off ;# don't couple langevin bath to hydrogens # Periodic Boundary Conditions cellBasisVector1 71.7553130 0 0 cellBasisVector2 0 69.1472640 0 cellBasisVector3 0 0 135.8807230 cellOrigin -0.1258862316608429 0.13252083957195282 -0.38146135210990906 wrapWater on wrapAll on # PME (for full-system periodic electrostatics) PME yes PMEGridSizeX 72 ;# manual grid definition PMEGridSizeY 72 PMEGridSizeZ 144 # Constant Pressure Control (variable volume) ;# normally for minimization and heat, using NVT, maintain the same volume of box #useGroupPressure yes ;# needed for rigidBonds #useFlexibleCell no #useConstantArea no #langevinPiston on #langevinPistonTarget 1.01325 ;# in bar -> 1 atm #langevinPistonPeriod 100.0 #langevinPistonDecay 50.0 #langevinPistonTemp $temperature # Output outputName $outputname restartfreq 500 ;# 5000steps = every 10ps dcdfreq 500 xstFreq 500 outputEnergies 500 outputPressure 500 ############################################################# ## EXTRA PARAMETERS ## ############################################################# # Fixed Atoms Constraint constraints on consref ../common/g1I8LA_leap.pdb conskfile ../common/constraint.pdb conskcol X ############################################################# ## EXECUTION SCRIPT ## ############################################################# # Minimization minimize 20000