# molecular system amber on parmfile clig.top ambercoor clig.crd firsttimestep 0 temperature 0 reassignTemp 10 reassignFreq 100 reassignIncr 1 reassignHold 300 # force field exclude scaled1-4 1-4scaling 0.833333 # nonbond interactions switching on switchdist 8.5 cutoff 10 pairlistdist 12 # integrator timestep 1 nonbondedFreq 2 FullElectFrequency 4 stepspercycle 20 #PME stuff cellOrigin 64.48 61.11 80.69 cellBasisVector1 125.00 000.00 000.00 cellBasisVector2 000.00 119.00 000.00 cellBasisVector3 000.00 000.00 158.00 PME on PmeGridsizeX 150 PmeGridsizeY 150 PmeGridsizeZ 160 # output outputname min1 outputenergies 100 outputtiming 100 binaryoutput no dcdfreq 1000 wrapall on wrapNearest on # for restarting: restartname min1-restart restartfreq 1000 restartsave no # position-restrained fixedAtoms on fixedAtomsFile minimize.pdb fixedAtomsCol O fixedAtomsForces on #constraints on #consRef 1.pdb #consKFile 1.pdb #consKCol B #langevin on #langevinDamping 10 #langevinTemp $temperature #langevinHydrogen on # #langevinPiston on #langevinPistonTarget 1.01325 #langevinPistonPeriod 200 #langevinPistonDecay 100 #langevinPistonTemp $temperature #useGroupPressure yes #useFlexibleCell no #useConstantRatio no extraBonds yes extraBondsFile 1_eb.txt # minimize fixed protein minimize 10000