Sample control file
Energy minimization with positional restraints on protein heavy atoms
In the initial structure, there may be artificial atomic crash in some parts of the system, which causes unstable energy minimization. The keywords contact_check = YES
and nonb_limiter = YES
allow us to avoid such situation. These options can reduce large forces on the crashing atoms. For details, please see the user manual ([ENERGY]
section).
[INPUT] topfile = top_all36_prot.rtf, top_all36_lipid.rtf # topology file parfile = par_all36_prot.prm, par_all36_lipid.prm # parameter file strfile = toppar_water_ions.str # stream file psffile = ionized.psf # protein structure file pdbfile = ionized.pdb # initial structure reffile = ionized.pdb # reference coordinates for restraints [OUTPUT] dcdfile = min.dcd # DCD trajectory file rstfile = min.rst # restart file [ENERGY] forcefield = CHARMM # CHARMM force field electrostatic = PME # Particle Mesh Ewald method switchdist = 10.0 # switch distance cutoffdist = 12.0 # cutoff distance pairlistdist = 13.5 # pair-list distance vdw_force_switch = YES # force switch option for van der Waals pme_nspline = 4 # order of B-spline in [PME] pme_max_spacing = 1.0 # max grid spacing contact_check = YES # check atomic crash nonb_limiter = YES # failure caused by atomic crash is avoided [MINIMIZE] method = SD # Steepest descent method nsteps = 5000 # number of minimization steps eneout_period = 100 # energy output period crdout_period = 100 # coordinates output period rstout_period = 5000 # restart output period nbupdate_period = 10 # nonbond update period [BOUNDARY] type = PBC # periodic boundary condition box_size_x = 128.000 # box size (x) in [PBC] box_size_y = 128.000 # box size (y) in [PBC] box_size_z = 144.000 # box size (z) in [PBC] [SELECTION] group1 = sid:PROA and heavy [RESTRAINTS] nfunctions = 1 # number of functions function1 = POSI # restraint function type direction1 = ALL # direction constant1 = 1.0 # force constant select_index1 = 1 # restrained groups